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6. Gene Growth 

6. GENE GROWTH 
The origin of new genes

6. GENE GROWTH
6.1 Aunt Adoption
6.2 Gene regulation
6.3 The Leapfrog Protein
6.4 Adoption 
6.4.1 Why is adoption absolutely necessary for evolution?
1. Darwin’s most primitive eye needs genes
6.4.2 Functional adoption and ‘function-acquiring mutations
1. Dead genes
2. The advantageous mutation
3. Free mutation
4. The Valley of Dead Genes
5. A hidden path? The distinction between different genes
6. The distinction between different genes
7. The Leapfrog protein is an essential protein which could not have evolved
8. The greater part of the genes does not vary at all!
9. Essential genes can differ greatly between non-related species
10. The Evolution Mountain Range
11. A bone to pick with E. coli
6.4.3 Metabolic adoption
6.5 Conclusions
In the previous chapter, we heard from the proponents of evolution themselves how macro-evolution theoretically would occur. Their words have seriously called the role of Master Crook Mutation into question, but there are a few people who are still not yet completely convinced. That is why I will try, in this chapter, to permanently settle the issue of Master Crook Mutation’s role as the (sole) cause of macro-evolution. That will immediately lay the foundation for dealing with his family members in chapter 7.
In order to have an idea of what we are discussing and to prevent unrealistic theoreticising and philosophising, we need to take a look at the way in which genes work together, and I will give a specific example of a robot protein. Afterwards, I will elaborate on the need for gene growth and adoption, because these are conditions of macro-evolution.
This is the most important, but also the most extensive and probably the most difficult chapter in the first part of the book. It might be helpful for the reader to read the summary which can be found in the Quick Tour in Chapter 18, in order to better understand the general line of this material.
6.1 Aunt Adoption
Do we know of a mechanism (like for instance natural variation) which takes care of gene growth? We will be applying ourselves to this question in this and the next chapter. This question is important, because the evolution theory says that there is (or has been) an increase in complexity. The ‘more highly developed’ animals originated from ‘less highly developed’ ancestors.[1] In the end, we are all descended from unicellular organisms. Bacteria have only one chromosome which has much less DNA than any other creature. How did this growth in DNA get started? No, that isn’t put right. How did gene growth get started? Where did the hundreds of genes come from that code for organs which were not there at first? If a species has 10,000 genes, what happens to make it 10,001 at some point in time, at finally 11,000?
The question is actually bigger than that: how did macro-evolution get started? But it is clear that gene growth [2] is absolutely necessary for macro-evolution, because the number of genes varies greatly from species to species. If evolution took place between species with a different number of genes, somehow, from their common ancestor onwards, growth or increase in genes must have taken place.
This means that we can already come to a conclusion about Master Crook Mutation’s potential uncle: whatever his name is, whoever he is, he is married to Aunt Adoption! But to understand who Aunt Adoption is, we need a better understanding of the way in which genes and proteins work.
6.2 Gene-regulation
Genes are not just pieces of DNA that code for a protein, and they also don’t spend all day just making proteins. Nothing happens until the moment they are needed. Transcription, or the translation of the code to the model (mRNA) that makes the protein, has to be turned on or off. The production of proteins has to be able to be sped up, or slowed down. Certain genes only have to work in specific organs. In the skin, no insulin, which is necessary to maintain the blood sugar level, needs to be made, for example. In short: genes need to be regulated. This happens through operators, promotors and repressors. A gene which codes for a protein needs other, different genes to work with, which regulate it. 
Below you can see an example of such co-operation of genes (called metabolism). Here you see the genes for lactose-metabolism in bacteria[3] during which lactose is broken down into the two sugars glucose and galactose. These serve as ‘food’. 
It is important to now study the figures below, before reading further. 

Figure (a). The order of the functional elements on the DNA
blue, i: The code of a repressor gene; when this piece of DNA is translated, a Turn-Off-This-Gene protein is made 
purple: Transcription never happens at just any place on the DNA. There is a special make-a-model protein (RNA Polymerase) that makes the copies(mRNA) for proteins. This Make-A-Model protein starts to make its model when it comes across the specific code on the DNA which indicates that the model starts there. The Make-A-Model protein can attach itself to that spot. That place is shown in purple and is called the promotor. 
green: The Turn-Off-This-Gene protein also has a place where it can attach itself to the DNA. This is shown in Green, and is called the repressor. 
brown,yellow,orange: These are the codes for the three proteins necessary to break down lactose. They are indicated by the letters z,y and a. 

Figure (b). inducer absent 
If there is no lactose present in a cell, Turn-Off-This-Gene protein is produced continuously, which attaches itself to the green piece of code where the Turn-Off-This-Gene protein fits perfectly. As a result, the Make-A-Model protein is incapable of attaching itself to the pieces of code it needs in order to make a translation to a model. No copies are produced and no z-, y-, and a-proteins are produced. 

Figure (c). Inducer present. Lactose is the inducer. 
The Turn-Off-This-Gene protein is still being made continuously, but this protein has a keyhole, where the lactose key, and only the lactose key, fits exactly. This locks the Turn-Off-This-Gene protein, so that it can no longer attach itself to the (green) piece of code. The Make-A-Model protein is now able to find the Model-Starts-Here code, and copies are being made. From these copies, the z-, y-, and a-proteins are then made. The z-protein is the Break-Down-Lactose protein. When the lactose is gone, the Turn-Off-This-Gene protein is no longer locked, which means that the production of copies ceases, so that it returns to the situation in figure(b). 

genes and their proteins co-operate closely 

You see here a mechanism which only comes into play when it is necessary. There are different kinds and degrees of mechanisms. Here, too, you can see that a protein can have various functions. The Turn-Off-This-Gene protein can sit on a specific location on the DNA with a specific code in order to thwart the Make-A-Model protein, but it also has a place where lactose can attach itself, so that it can be locked.[4] In order to fit itself to the DNA, this protein needs a three-dimensional structure which fits into the DNA spiral precisely, and then a few very specific amino acids at the right locations, which attach to very specific bases (A, C, G, or T). This is applicable to the Break-Down-Lactose protein, which has to be able to pick up lactose, and needs the right molecular tongs for that, to cut it in two at the right places. The y-protein is a Transport-Lactose protein. It can pass through the cell membrane to the outside, handcuff a lactose molecule, subsequently passing through the membrane again on the way in, because it has the right ID card, and there it releases the lactose again, so that it can be broken down by the Break-Down-Lactose protein. Now that’s working together!
gene teamwork works with ID’s and keys

Nothing in a cell happens by itself! Everything is arranged by proteins. All proteins are made by the cell itself. All proteins co-operate. One does this, the other does that. One arranges it that the other comes into play when it is necessary, the other arranges it so that yet another does something else. It is hopelessly complicated! It is also admirable that humans are capable of unravelling tiny pieces of the mystery time and again.

Figure 2. A molecular key: because the Signal protein (drawn as rods) fits exactly into the lock of the larger Receiver protein, (chemical) action is initiated (or not).


Figure 3. GLUT1 (green) is a Transport protein which recognises the ‘ID’ of glucose (red) and therefore allows it to pass through the cell wall. It is a Bouncer-for-a-Private-Club protein. 


Figure 4. Biochemistry, pp. 880; Leapfrog protein 
The point here is that a gene does not stand alone. One gene is nothing. One gene is only good for one protein. That protein has to do something very specific if it wants to be useful. That protein has to be active at the right place and at the right time. For that purpose, it needs other proteins and therefore other genes. I will call this gene teamwork. Gene teamwork says that one gene on its own is useless. Genes have to work together, be in tune with each other. If a Turn-Off-This-Gene protein suddenly (due to a mutation) no longer feels like binding lactose, then it goes very wrong, then all those other genes (z, y, and a) also do not act. Or if the Turn-Off-This-Gene protein suddenly attaches itself to a molecule other than lactose, the whole system is thrown into disarray. That is why such proteins have keys, so that they can only attach themselves to lactose. They have, as it were, gotten a certificate of uniqueness: there is absolutely no other molecule which fits.
So gene teamwork is full of unique keys, because in a cell, all sorts of molecules are jumbled together. If there were no keys, how would such a soup of proteins ever be able to work well? And a lot ofproteins have ID cards. Some are allowed to go outside, others are not. Yet others can bring others inside, or outside. Some have to be inside special buildings in the cell (with names like mitochondria or Golgi apparatus), or be brought out of those buildings. Intruders are unwelcome in these specialised factories, so you cannot enter without an ID or a guide. Teamwork. Rules of the game. Keys. Agreements. Locks. Pre-programmed or programmed.
6.3 The Leapfrog Protein
Now that we have gotten a hint of how genes work together, we are going to take a look at a concrete example of a protein-robot. That is practical because it is important to know what we are actually talking about when we discuss a ‘protein’ (and the gene behind it). 
Tug-of-war
When a cell splits, resulting in two identical cells, the DNA is copied during that process. The two strands of DNA are pulled apart and the corresponding bases are added to both sides, resulting in two identical DNA molecules. This is a process that is intensively monitored by all sorts of proteins. One of those is the Leapfrog protein, which is actually called Topoisomerase.
Suppose you take a piece of rope a few meters long. You knot one side firmly to a chair, and you split the other side in two. Next you pull those two pieces apart. What happens then? The rest of the rope is rolled up very tightly and curls up on itself and gets all knotted up. That happens to DNA too, and that is not permissible. If the tension gets too great, it can break, or if it gets knotted, it can no longer be duplicated.[5] 
How does that work? Well, that is where the Leapfrog protein comes in. The Leapfrog protein has two large arms for gripping, one on top and one on the bottom, which together form the shape of a C. It takes hold of one half of a DNA strand with both paws right next to each other. It cuts through that half of the strand, but keeps hold of the ends. It then rotates the two cut ends in different directions toward the other side, and in the meantime lets the second half, as it were, inside, so that it embraces the strand. Then it glues the two cut pieces back together. When that has happened, it lets go and begins again there or somewhere else. In this way, the Leapfrog protein can take one entire DNA strand straight through another, so that unravelled DNA does not come to resemble a piece of yarn so entangled that is impossible to de-tangle it.
In figure 5 is a computer representation of the Leapfrog protein and how it cuts a strand of DNA and lets another through. As you can see, it is a highly specialised molecular robo

Figure 6.the Leapfrog Protein at work 
A. Leapfrog protein at rest. 
B. The Leapfrog protein attaches itself to a single strand of DNA (green) at the red dot. 
C. The strand is severed and the Leapfrog protein opens up. 
D. Now a double (as in this case) or single strand of DNA can be allowed to pass through. 
E. The two sections of the severed DNA strand are glued together again. 
F. The Leapfrog protein opens again. 
G. The ‘imprisoned’ strand of DNA can get out.The process can start again, or the Leapfrog protein returns to its resting position. 
6.4 Adoption
What does adoption mean? There are two forms of adoption to be distinguished from each other. When a protein, for instance already mutating, changes function and takes on a new, different function (which it did not already have), it adopts that new function, as it were. I will call this functional adoption. This is therefore no mere small alteration in which the same functionality remains, but is carried out differently, faster, or less, or better, etc. That is only a functional change or even damage. Functional adoption could perhaps be an accumulation of functional change, but if functional adoption is being discussed, the original function has to differ structurally or be essentially different from what it was before. It has to adopt a different, new function that it did not have at first, and it has to expand to the same refined degree of specialisation as the Leapfrog protein. Functional adoption is therefore specialisation, in which the whole structure of the protein is such that it is optimally equipped for its task, as is the case with all 100,000 genes in our cells!
Therefore, it is not even a question of functional adoption if a few amino acids change so that the existing protein suddenly has an effect on something that it previously did not have. That is throwing a wrench into the workings of another refined mechanism. Only if the protein became specialised in that function and all the parts were in tune with that function could you speak of functional adoption.
The second form of adoption is that a new gene (for instance a gene in which functional adoption has taken place) is adopted into the family of co-operating genes, in other words has to be regulated, turned on and off at the right time. For such an adoption, many other genes are necessary, such as, for instance, a regulator gene, a ‘binding site’ it can attach itself to, a promotor and/or a repressor, and such. This kind of adoption I call metabolic adoption. If the six genes of lactose metabolism as it is described above were to have developed from another metabolism that once did not have that functionality at all, then you could speak of metabolic adoption: A protein which has gone through an essential functional change has to be taken into some new chemical balance, process, mechanism (called metabolism).
6.4.1 Why is adoption absolutely necessary for evolution?
Although we have already looked at some arguments for why adoption is necessary, I will still give an extensive example here of why gene growth and the adoption it entails are absolute conditions of macro-evolution, the change from one species or type to another.
1.Darwin’s most primitive eye needs genes 
As an example, take the classic argument of the eye, which has been used before by Darwin and many others after him. Is there something new to be said about it then? Is there anything to be added to the discussion which has not yet been said? Yes, there certainly is, because we can now look, on the lowest level of evolution, the level of DNA, at genes and proteins to see how an eye could have developed. Darwin did not have that option. We no longer have to speculate or even fantasise about what is and is not possible. On the DNA level, the possibilities and chances can even be calculated! So, let’s have a look.
Darwin says this: 
If we must compare the eye to an optical instrument, we ought in imagination to take a thick layer of transparent tissue, with a nerve sensitive to light beneath, and then suppose every part of this layer to be continually changing slowly in density, so as to separate into layers of different densities and thicknesses, placed at different distances from each other, and with the surfaces of each layer slowly changing in form. Further we must suppose that there is a power always intently watching each slight accidental alteration in the transparent layers; and carefully selecting each alteration which, under varied circumstances, may in any way, or in any degree, tend to produce a distincter image. We must suppose each new state of the instrument to be multiplied by the million; and each to be preserved till a better be produced, and then the old ones to be destroyed. In living bodies, variation will cause the slight alterations, generation will multiply them almost infinitely, and natural selection will pick out with unerring skill each improvement. Let this process go on for millions on millions of years; and during each year on millions of individuals of many kinds; and may we not believe that a living optical instrument might thus be formed as superior to one of glass, as the works of the Creator are to those of man?[6] 
It is not hard to imagine. Close your eyes and try to see it before you. It can work. If that doesn’t work, the current computer programs might help. It is called morphing. Michael Jackson started it in a video clip, later advertisements followed, and these days you can buy simple programs which any amateur can put on their computers. You see an old man’s face transform fluidly into the face of a child, an African into a European, a woman into a man, a human into a panther. It is not hard to imagine that a layer of transparent skin with a light-sensitive nerve under it develops into an eye like a human’s. You can even make a computer animation of it. Except, Darwin knew nothing about genetics...
What does an organism need, an organism which does not yet have anything resembling an eye, to begin to develop one? Genes! Genes arrange the development of the eye during embryonic growth, genes maintain the eye, genes arrange the processes in the eye, in the nerves, in the brain which turns that light into a picture that our mind understands. Nothing in a cell happens by itself. That takes proteins and genes that code for those proteins. And all those genes have to come from somewhere. They don’t need to all end up in an organism at the same time, but, if evolution is going to happen, there does need to be an increase in genes which do this. In the beginning, it will be a few, the ones which make a nerve cell appear at the right place, and the ones which ensure that it is built in at the right moment during embryonic development and the ones which take care of communication with the brain and the co-ordination with the rest of the body. There is no point to this process if a stimulus from that primitive ‘eye’ does not become ‘conscious’ in a certain way, so that it can be reacted to. A photosensitive spot on my big toe is of no use to me if I cannot receive the signal in my brain, so that I can do something with it. Let us say that the most primitive form of the eye, as Darwin suggested it, needs ten genes. This is a bit less than is actually needed, but we have to start somewhere. I will propose this very simplistically the first time, in a way which does not do justice to the complex reality of genes. However, if I do it in a highly simplified way, it will in any case be clear to everyone how necessary gene growth is for evolution.
Name of the gene Function
Transparent This gene ensures that a cell becomes transparent.
Make-Transparant This gene ensures that the production of transparent genes begins at the right time during embryonic development.
At-This-Place This gene ensures that transparent cells are produced at a specific place and not arbitrarily spread throughout the organism.
Size-Gene A gene that determines the size of the transparent tissue, where it starts and where it stops.
Nerve-Gene This makes a cell a nerve cell.
Photosensitive This gene makes a cell sensitive to light.
Make-Nerve At the right moment during embryonic development, one or more cells have to form nerves.
Nerve-At-This-Place The nerve has to be placed exactly under the transparent tissue.
Connection Gene The nerves have to go from the eye to the brain.
Signal Gene A signal has to be able to pass along the nerves, and some form of ‘consciousness’ has to be present to be reacted to.

Here you see the ten genes. In actuality, the number of genes is a multiple of what is named above, even for a minimal primitive eye (see Box). However, it is clear that it is necessary that these genes are formed in some way, have to originate in the DNA of an organism, if a new organ, like an eye, is to be able to grow. Next, a steady increase in the number of genes for this eye is still necessary, because hundreds or even thousands of genes are necessary for the most complex eye there is.
Box: The twelve proteins which make a cell sensitive to lightThat follows is part of an article by Michael Behe on the true complexity of ‘sight’: In general, biological processes on the molecular level are performed by networks of proteins, each member of which carries out a particular task in a chainWhen light strikes the retina a photon is absorbed by an organic molecule called 11-cis-retinal, causing it to rearrange within picoseconds to trans-retinal. The change in shape of retinal forces a corresponding change in shape of the protein, rhodopsin, to which it is tightly bound. As a consequence of the protein's metamorphosis, the behavior of the protein changes in a very specific way. The altered protein can now interact with another protein called transducin. Before associating with rhodopsin, transducin is tightly bound to a small organic molecule called GDP, but when it binds to rhodopsin the GDP dissociates itself from transducin and a molecule called GTP, which is closely related to, but critically different from, GDP, binds to transducin. The exchange of GTP for GDP in the transducinrhodopsin complex alters its behavior. GTP-transducinrhodopsin binds to a protein called phosphodiesterase, located in the inner membrane of the cell. When bound by rhodopsin and its entourage, the phosphodiesterase acquires the ability to chemically cleave a molecule called cGMP. Initially there are a lot of cGMP molecules in the cell, but the action of the phosphodiesterase lowers the concentration of cGMP. Activating the phosphodiesterase can be likened to pulling the plug in a bathtub, lowering the level of water. A second membrane protein which binds cGMP, called an ion channel, can be thought of as a special gateway regulating the number of natrium ions in the cell. The ion channel normally allows natrium ions to flow into the cell, while a separate protein actively pumps them out again. The dual action of the ion channel and pump proteins keeps the level of sodium ions in the cell within a narrow range. When the concentration of cGMP is reduced from its normal value through cleavage by the phosphodiesterase, many channels close, resulting in a reduced cellular concentration of positively charged sodium ions. This causes an imbalance of charges across the cell membrane which, finally, causes a current to be transmitted down the optic nerve to the brain: the result, when interpreted by the brain, is vision. If the biochemistry of vision were limited to the reactions listed above, the cell would quickly deplete its supply of 11-cis-retinal and cGMP while also becoming depleted of sodium ions. Thus a system is required to limit the signal that is generated and restore the cell to its original state; there are several mechanisms which do this. Normally, in the dark, the ion channel, in addition to sodium ions, also allows calcium ions to enter the cell; calcium is pumped back out by a different protein in order to maintain a constant intracellular calcium concentration. However, when cGMP levels fall, shutting down the ion channel and decreasing the sodium ion concentration, calcium ion concentration is also decreased. The phosphodiesterase enzyme, which destroys cGMP, is greatly slowed down at lower calcium concentration.Additionally, a protein called guanylate cyclase begins to resynthesize cGMP when calcium levels start to fall. Meanwhile, while all of this is going on, metarhodopsin II is chemically modified by an enzyme called rhodopsin kinase, which places a phosphate group on its substrate. The modified rhodopsin is then bound by a protein dubbed arrestin, which prevents the rhodopsin from further activating transducin. Thus the cell contains mechanisms to limit the amplified signal started by a single photon.Trans-retinal eventually falls off of the rhodopsin molecule and must be reconverted to 11-cis-retinal and again bound by opsin to regenerate rhodopsin for another visual cycle. To accomplish this trans-retinal is first chemically modified by an enzyme to transretinol, a form containing two more hydrogen atoms. A second enzyme then isomerizes the molecule to 11-cis-retinol. Finally, a third enzyme removes the previouslyadded hydrogen atoms to form 11-cis-retinal, and the cycle is complete.Twelve specialised robot-proteins are needed just in the photosensitive cell, in order for it to become sensitive to light at all. Seeing colours is another matter altogether. Besides, the details are not mentioned in the above description. It is clear that the lack of one single protein in this process would cause blindness. The question is: now that we know how it works, how did this mechanism originate? 
gene growth is absolutely necessary 

It is clear, gene growth is necessary, but a general increase in genes by itself is not enough. Functional adoption is also necessary. If an organism has no nerve cells and these nerve cells need to originate, then not only does the number of genes need to increase, but completely new functions must also be carried out by these genes, which had never been seen before. Proteins must be produced which have never been produced before. Robots need to appear which can do things that have never before been possible. A new gene must therefore also acquire a new useful function, or adopt one. Such a new function, for instance React-To-Light, or the function Make-A-Cell-Transparent, must also be regulated, that is: it must be adopted by the community of genes which is already in place, so that it will carry out its function at the right time and in the right place. Not only does a group of genes work together, groups of these groups work together in an organ, and those organs have to co-operate with all the groups of co-operating genes in other organs. Before an organ can function at all, and before the useful proteins in that organ are able to fulfil their functions, groups of co-operating genes have to have built that organ during the development of the embryo.
These three, therefore, gene growth, functional adoption, and metabolic adoption must be structurally possible if evolution on a large scale (macro-evolution) is going to be able to take place. Because evolution is, in the first place, arbitrary, such an infinite amount of variations on new (co-operative) genes needs to arise, as it were, that natural selection has more than enough to choose from to get the kind of specialisation and the level of co-operation that we observe in living organisms.
With this, the difference between micro-evolution and macro-evolution becomes clear almost immediately: macro-evolution could be (at least) defined as ‘the origin of new groups of co-operating genes which fulfil functions which have not previously been observed in that organism’. All other alterations in or combinations of existing genes are thus variation on a theme or micro-evolution, because through that by itself, nothing fundamentally new will be added.
6.4.2 Functional adoption and ‘function-acquiring 
mutations’ 
What we are going to do now is look at how a protein, already in the process of mutating, can grow towards another function, in other words how functional adoption would arise. This accumulating, gradually mutating change towards another function I will cal gradual adoption, in contrast to the radical leaping transition to a new function, which is also called leaping adoption. The latter is covered in the next chapter.
In Genetic analysis on pp. 794 under the heading [Het ontstaan van nieuwe functies] is the only(!) example given in all of my sources: B. Hall has experimentally changed a gene to a new function in Escherichia coli[7]. In addition to the lacZ genes specifying the usual lactose-fermenting ß-galactosidase activity in E. coli, another structural gene locus ebg specifies an other ß-galactosidae that does not ferment lactose, although it is induced by lactose. The natural function of this second enzyme is unknown. Hall was able to alter this gene into one specifying an enzyme that ferments another substrate, lactobionate. To do so, it was necessary to alter the regulatory element to a constitutive state and to produce three successive structural-gene mutations.
Does this not show clearly and convincingly enough that functional adoption is possible? Or does it? (The answer follows under point 11.)
1. Dead genes
Dead genes genes can lose their function by mutation
Genes can lose their function so that they no longer have any function, though they may still code for a protein. Recessive inheritance of a characteristic often indicates that:
A recessive allele often has lost part or all of its ability to perform the function of the normal allele. In a heterozygote, one copy of the dominant allele may provide enough of a given gene’s normal function to support the development of a normal phenotype. Thus in a pea plant heterozygous for round seed trait (Rr), the single R allele allows enough of a specific enzyme to be synthesized so that sufficient starch is manufactured to give a firm, round appearance to the seed. In a homozygous recessive plant (rr) , the protein controlled by the r allele is not enzymetically active, so that not enough starch is produced to make the seed plump, and it appears wrinkled.
Biology, pp. 246. 
One single mutation is capable of paralysing a gene completely. Consider the Leapfrog protein. Suppose a mutation causes an amino acid in one of his claws to change, which makes him unable to take hold of the DNA strand (firmly). As a result, the entire protein can no longer work. That one mutation will cause the protein to become a dead protein or the gene a dead gene.[8] Now the Leapfrog protein is so essential to the functioning of a cell that living creatures will never occur with a dead Leapfrog gene.[9] In practice, that usually means that at a certain point the development of a fertilised egg cell cannot continue and the embryo dies.
On the other hand, it is also possible for a certain mutation not to bring all the functions of a protein to a stop immediately, because the change in base pairs does not make much difference in the amino acids, or because it is in a less essential part, or because the protein’s function only decreases partially. However, an accumulation of mutations will eventually result in the protein becoming totally defective. In other words, to the left, to the right, before and behind this ‘mutating protein’[10] lie yawning chasms with sheer, deep walls. As soon as the protein goes one step (i.e. mutation) too far, it loses its function and the mutant falls into the precipice next to it and dies. The protein is, as it were, on a mountain peak. Only on that peak can it do what it needs to do. If it descends too far, it loses its original function.
(The question of whether (hidden) paths can be found on that mountain will be covered in point 5.) 

Figure 6, The Mount of Isolation: only on the uppermost surface does the protein retain enough of its function not to be a ‘dead’ protein.
2.The advantageous mutation
Now we get into an important matter which Master Crook Mutation conceals from us and where confusion of terms sets in, since he says that he can make new characteristics and is a source of variation. What happens internally on the DNA level? 

the loss of a gene can benefit its carrier
When a protein has lost its function, it is quite possible that that the individual in which it lives benefits (!!) from it. Think for instance of the loss of skin colouring in an Arctic fox, which gives it a white pelt. That is a definite benefit to the fox in the snow. However, it is not the protein itself which has undergone a ‘change in function’. It is not the protein itself which causes a ‘new characteristic’ to appear. It is the loss of that protein that cause a ‘new characteristic’ to appear! This so-called ‘new characteristic’ can be advantageous, but the protein has not become ‘better’ for those circumstances. The protein has been lost, or damaged so that it can only do half of its work.
As long as the protein is fine and functioning, selection can take place for that functioning-of-the-protein, but as soon as a protein becomes a dead protein, the selection for the protein itself disappears. Selection can continue to exist for the absence of that protein, or its non-functioning.

in dead genes, selection no longer takes place on the protein sequence
It is important to make that distinction and to understand it thoroughly. As soon as a gene has lost its original function, even if that benefits the carrier, the pressure of selection on the functioning of that protein disappears, and related to that, the selection pressure on the structure of the protein, which is determined by the sequence of the amino acids. In other words, to put it succinctly, the selection pressure on the sequence of amino acids disappears.[11] This is because it no longer matters if the protein ceases to function 100%, or ceases to function 50%. In both cases, it no longer functions. It then also no longer matters what kind of protein is being coded for, or even if a protein is being coded for. Each successive mutation can damage the protein further, it no longer matters. The protein has died. It has become a dead protein. The is no more selection which preserves the protein sequence, the order of the amino acids in the protein. The gene is delivered into the hands of ‘free mutation’, which means mutation-without-selection.

a distinction needs to be made between micro-evolution and molecular evolution
The reason that this is never fully understood is that the distinction is not made between the evolution of proteins, or the protein sequence, on the one hand, and the evolution of an individual or a species on the other hand. Because, again: selection can happen for the loss of a function in a protein, but the selection for one mutation instead of another in the protein itself has then disappeared.
For instance, it is said that: ‘a mutation causes a new characteristic’, or ‘mutations are the source of variation’. However, such statements do not take the difference between levels of evolution sufficiently into account. A mutation, which causes a ‘new’ characteristic and therefore gives rise to ‘new’ variation, can, speaking genetically, quite possibly have completely eliminated a gene. In that case, that mutation is totally not a source of variation, but a vessel which draws from the source, by removing something!
This is the confusing effect of a mutation if no distinction is made between the levels of evolution:
level the effect 
1. micro-evolution A mutation causes a new characteristic. 
This is the clarifying effect of a mutation if the levels of evolution are clearly distinguished from each other: 
level the effect 
2. variation + natural selection A 'new' characteristic is signalled. 
1. molecular evolution A mutation damages a gene or even eliminates it. 
Because of this, fruit flies in my compost are not seen. If I were to breed them and expose them to strong UV light so that some serious mutations happen, at some point in time, I could see some fruit flies with white eyes. A mutation has, as it were, pulled this new characteristic out of thin air. However, genetically speaking, a functioning protein has been put out of commission, namely the protein which would usually make red pigment in the eyes.
3.Free mutation. 
As long as a protein continues to perform a useful function, selection for the protein sequence can take place. If a mutation changes the sequence of amino acids, thereby changing the function, thereby changing ‘something’ in the carrier of that gene, then one sequence can be chosen instead of another by natural selection.
free mutation means no evolution
What does that mean for a protein, that it is no longer selected for and that it can mutate freely? That that protein no longer evolves!
Because it went like this: 
arbitrary mutation + non-arbitrary selection = evolution. 
If selection is no longer possible, because the protein is dead, there is no longer evolution in that protein! 
arbitrary mutation + no selection = no evolution 
It is an absolute condition for a ‘mutating protein’ that it never loses its function completely and becomes a dead gene. If it dies and can mutate ‘freely’, suddenly, all the rules of that absurd calculation of probabilities comes into effect which say that the chance for a coincidental new functional protein is 1 in 20300. Suddenly, the laws if King Entropy come into effect!
If a protein crosses the line of useful-functionality, because it moves downwards through the mist, then the Kingdom of King Entropy enters, the land of the dead, where another law applies than on the peak of the mountain. On top of the mountain, it is light. the Angel of Natural Selection rules, but below the peak, underneath the mist of functionality, it is dark, Fool Coincidence plays with amino acids and King Entropy calls the shots.

King Entropy’s strengthFigure 7 is a typical example of the decreasing order in the protein of a freely mutating gene, made up of 100 amino acids. On the X-axis is the number of mutation, on the Y-axis the percentage of correspondence with the original protein (1 altered amino acid is 1%). The calculations were made by repeatedly allowing an arbitrary mutation to take place in one of the base pairs of the gene, and then to take a look at the degree of correspondence with the original protein.All plateaus (the longer or shorter horizontal lines) are caused by mutations which have no effect, they continue to code for the same amino acid, which is caused by the structure of the genetic code. An abrupt drop is caused by the appearance of a code for a stop signal. That results in a large part of the protein not being made any more. The chance that a stop signal will appear is 1 in 64, and therefore can occur several times in a graph of 250 mutations. The sudden increase in order is caused by a previous stop signal coding for an amino acid again, which results in the protein regaining its original length. However, it is clearly visible that despite the return of the tail, the order in general just continues to decrease. Every once in a while, a small increase can be seen. That is the work of Fool Coincidence who causes a wrong amino acid to become the right one again, which makes the graph rise 1%. The chance of that happening is bigger the more disordered it gets! The descent for the first 10 mutations is thus always steeply downwards. As order decreases, the plates become longer and the chance for a single percent increase becomes larger. 
Figure 7, example of the decrease in order in a ‘freely’ mutating protein
All of this shows King Entropy’s power. If I let my computer make this sort of calculations for the next five billion years, there would still be no increase in order, not even if I would enter all the possible useful combinations of amino acids, simply because the number of useful combinations pales in comparison to the number of useless combinations (see below).[12] 
It is of the UTMOST IMPORTANCE that this argument – no new devoted, specialised genes originate through free mutation, or by sheer coincidence - is realised and understood. It is the essence of my argumentation, which by the way is completely in agreement with what the proponents of the evolution theory say themselves. (see 5.1.a).
Still, many people are not aware of this fact (or convinced of it!), as the conversation I had with a respected biologist makes clear: 
H.R. : There is a lot of DNA which does not code, which doe snot have any function at this point in time. That does not mean that it cannot be switched on at any given moment. A gene which does not have a function at first can get a function by mutation.
Peter: But if it has no function, then it is also not selected for?
H.R.: No, then it is just hitching a ride. A great deal of your genetic material has no function at this point in time, but can gain a function at any moment. It is a reservoir which can be accessed at a time when that serves a purpose.The parts of the DNA which do not code for anything right now have all the freedom possible to mutate, without it having damaging consequences for the organism. That is the incubator for new characteristics. At a certain point in time, part of the DNA which is in that incubator can add a characteristic to the characteristics which already exist.
King Entropy says: 'NO WAY!' to this biologist.
In the first place, it is still not certain that DNA which does not code for proteins has no function. (see ch. 12) Apart from that, nothing originates by coincidence alone anyway, not even in the dead genes which no doubt can be found in the DNA. A protein made up of 300 amino acids (‘a little one’ according to this biologist) has 20300, that is 10390 possible combinations, which in comparison to the 1080 atoms in the universe is infinitely great. On the other hand, a human has at most 100,000 genes (or 105) which have a useful function. If you then assume that there are 100 million species (which is on the high side), that these genes are all different (which is absurd, since many genes are the same), and that over the course of five billion years, each year there have been that number of species with that same number of functioning genes (which is obviously not true), then there would be 5 x 108+5+9 is a maximum of 1023 functional genes.
That this number is larger than is realistic is due to the face that, theoretically speaking, each new protein has to build on what already exists. Not just any combination of amino acids can do something useful in a living organism. On the contrary, it has to have a precise structure in order to fill a specific function and to be able to work with other genes. It has to ‘fit’ in the structures and co-operations which are already present. That means that only a very small number of combinations can be useful in a specific species and that 1023 is somewhat exaggerated. Another indication of a very low number of useful protein sequences is the high number of damaging genes a mutation has had: only a very precise combination of amino acids has a useful role to play in living organisms, and the rest are discarded.
However, as yet we will suppose that there are still that many possibilities. The chance that a functional gene originates from a gene which was at first not functional by coincidence, is 1023 in 10390, which is 1 in 10367. That last number is still infinitely greater than the number of atoms in the universe and will therefore not have occurred even once in five billion years, or, if we give Fool Coincidence the insane benefit of the doubt: ... once.
Pure coincidence is in no way a useful mechanism for the origins of new genes. The only remaining option is that new genes evolve from existing genes (or copies of existing genes).
If the reader is still not convinced of this, there is no point in reading the rest of this chapter (or the next). For those readers, I will now describe a game which can occupy them until they are eventually convinced of the contrary:
Here is a description of a ‘protein’ with 142 amino letters (for which some 10185, which is infinitely many, combinations are possible):
nonewusefulspecialisedproteinsorproteinsequenceswilleveroriginatebypurecoinci
dencenotfromthednascrapheapandnotfromexistingproteinsjustnotatall
At some arbitrary (so not chosen) point, change a letter into an arbitrary, coincidental other letter, for as long as it takes until, no matter what it takes, the sentence reads that something useful can originate by pure coincidence (we just imagine the spaces, and no letters can be added or removed, only replaced). This game is closely analogous to ‘mutating proteins’, because the number of letters (20-26) is comparable to the number of amino acids and the number of nonsense-combinations in relation to the number of useful combinations is even smaller than in proteins, so that the chances of success increase.If enough people (or a few computers!) try it for long enough, surely it will work at least once...
Now there will probably be people who want to steal my thunder. That’s right, they will say, nothing useful originates through pure coincidence. But a small word can originate through coincidence. By ‘selecting’ that word and not selecting for each subsequent change in that word, and to continue like that until another new word appears somewhere, etc., at some point in time a lovely new sentence will appear. And of course, they are absolutely right!
However, the mechanism which is applied there is that of coincidence-plus-selection. The point we are at in the discussion is that of coincidence-without-selection. What I am asking of the reader is that he admits that coincidence-without-selection does not result in new proteins, not that he admits that coincidence-PLUS-selection does not result in new proteins. The central question which follows is, from what point onwards can selection occur? Can it occur from the point at which coincidental ‘words’ appear in a protein? Or can selection only occur when a more-or-less legible sentence is formed? In terms of proteins, that question means: From what number of protein combinations onwards is there a case of some useful functionality? Or, to put it differently: From what point at the foot of the Mount of Isolation can the Angel of Natural Selection start his work?
Well, I am sorry to have to say this, since it means that the reader who does not wish to follow me on this point will have to be left hanging with the above sentence for the rest of his days. but the smallest known proteins are about 100 amino acids long. The largest proteins form, from a molecular point of view, gigantic mountains, complexes, cathedrals of thousands of amino acids, but we will leave those out of the thick of this argument. In the here and now of biochemical daily life, the smallest useful proteins are about one hundred amino acids long. Later we will see that, in many case, the border in the foothills of the Mount of Isolation, from which point on the Angel of Natural Selection is able to do his work, is much higher.
As far as our game is concerned, this means that selection can only take place from about 100 letters on, because that is the first point at which any kind of functionality can be discussed.You are thus only finished when there is a complete and legible sentence of at least one hundred letters. We will overlook a few grammatical errors...
As encouragement for the persistent folk: there are lots fewer proteins with a length of around a hundred than there are possibilities to say that functional proteins can originate through coincidence with a 142-letter sentence. Compared with that, the chance that the above game will result in a proper sentence is larger than the chance that, in reality. a functional protein of about 100 amino acids will originate.The choice is yours: keep playing or read further?
4.The Valley of Dead Genes 
In Figure 8, three proteins are portrayed, two of which are closely related to each other. This is because it could be possible for the structure of a certain protein to be so close to that of another protein that it could change into the other protein through mutation, without ever, at any point in time, losing its functionality to such a degree that it becomes a dead gene. This is depicted by the second peak next to the first, which, albeit through a small dip, can be reached without descending beneath the highest border, the ‘line of death’.
In that case, it is conceivable that a protein could mutate from one peak to another, if the Angel of Natural Selection selects for that, at any rate. It is by the way a dangerous undertaking. One step too far across the border and the protein slips through the fingers of the Angel of Natural Selection, and immediately ends up in the valley of dead genes. Is this true? Is the Angel of Natural Selection so powerless on the other side of the border? Yes it is, take a look.

Figure 8, The Valley of Dead Genes 
proteins die a thousand deaths
The white-eye allele ( for fruit-flies, PMS) appears to cause a complete loss of normal gene function and thus an absence of eye pigment, while the other alleles cause a less drastic alternation of the normal gene function, and so the eyes contain different amounts of pigment. (…..) In fact, over 100 alleles of the white-eye gene have been discovered. Biology, pp. 247 
As you can see, there are more than a hundred ways in which a protein can die, but there are only a few in which it can do what it has to do. If a protein, because of one or more mutations, falls below the functionality border and thus enters the kingdom of the dead, the organism loses the function which it performed. However, it makes no difference if the protein dies in one way or in another.In other words, a small peak with limited freedom of movement rises above the mist, and all around (the other hundred versions, the ones with different alleles) are gaping chasms.
resurrection is only possible in the beginning 
Now the protein cannot simply be brought back to life. If a mutation happens in that gene again, it is a chance of 1 to 3 in 2700 (in a protein which has 300 amino acids[13]) that the right amino acid returns. In other words, there are at least about a thousand ways to destroy it further and one to restore it to its previous state.[14] This means that, after the first step across the border, the protein can only re-conquer its original function in very rare cases. After the second step across the border, the chance is 1 in 1,000,000 and only goes downhill from there. As soon as the border has been crossed, King Entropy’s dogs come after the protein. There is almost no escape. Once arrived at the bottom, King Entropy’s law applies: it is not permissible to take on any semblance of order.
In general terms, you can thus say that after one mutation across the border of functionality, there might be a way back through pure coincidence, but that after two or three mutations, the protein is so far gone that the way back is no longer a realistic option. In other words, the mist which hangs about the border of the kingdom of the dead is one or two mutations thick.
protein C is inaccessible
The third ‘mountain’ in the figure is a protein which differs structurally so much from the other two that it cannot be reached by mutation without losing its functionality and therefore becoming a dead gene which is not selected for.
Protein A can, as long as there is sufficient selection for it, mutate into protein B. Along the way, there will be many unfortunates who mutate in the wrong direction, but with sufficient selection pressure and sufficient time, it is possible. However, neither A nor B can mutate into protein C. Before they could get there, they would have to pass through the Valley of Dead Genes. And, as we have seen, King Entropy does not release his prisoners, so it is in no way possible for a protein, without the pressure of selection, to mutate ‘upwards’ along the steep cliffs to protein C.
Darwin’s driving force, called natural selection, has no jurisdiction in the valley of dead genes!
5. A hidden path?
If you read about a ‘function-acquiring mutation’ (see ch. 5.f), you do not get the impression that it is such a problem for a protein to take on another function at all. Why not? Because the landscape looks different, more like Figure 9. 

Figure 9, the Mount of Connectedness 
The suggestion created by the name ‘function-acquiring mutation’ as the engine for evolutionary change is that ALL those different peaks are joined together in some way or another, that an already-mutating protein never has to completely lose its function, step across the border of the kingdom of the dead, and in this way, without ever leaving the jurisdiction of the Angel of Natural Selection, can achieve another function, and from that function another and another.
The question is, therefore, which is closer to reality? Gently sloping hills with, it is true, a border with the kingdom of the dead, but nevertheless full of peaks and connections through which every protein can be reached in some way or another, or isolated peaks surrounded by steep crags?
For evolution to (have) work(ed),[15] each protein must be accessible from another protein (see Graph 1), through an accumulation of small changes in function and without ever losing its function to any significant degree, which would cause the selection pressure to disappear. 
Graph 1, Uninterrupted increase in functionality is an absolute condition 
In other words, there has to be a traceable path from every protein to another protein without it becoming a dead protein in between. In other words, every peak of the mountain has to be able to be uninterruptedly connected with another peak without ending up under the selection border (see Graph 2 and 3.) 
Graph >2, Interrupted increasing (or changing) functionality is an impossibility 
In reality, matters are really this clear-cut: if even one such protein can be found which stands on an isolated peak, without any connection to other peaks, it is already proven that structural evolution is impossible! We will call a protein which fills these specifications a Lone Ranger. 
Graph 3,Another example of impossible interrupted increasing (or changing) functionality 


6. The distinction between different genes
Let us then take a closer look at an organism’s genes, to see what their ‘adoption-mountains’ look like, and if their structure allows changing to another function. 
there are essential genes
Genes can be divided into three groups. There are genes which are so essential to the organism’s development into an adult individual capable of reproducing itself that that gene must not die. If Master Crook Mutation is able to pull such a gene across the border to the Valley of Dead Genes, not only does the gene die, but the carrier of the gene dies. In practice, this means for instance that the embryo does not develop and a spontaneous abortion occurs, or that the individual dies of its genetic defect before it is able to reproduce itself. This kind of genes we will call essential genes, in the sense that they are essential to the viability. An example of such a gene is for instance our Leapfrog protein (in reality it is called Topoisomerase), or Make-A-Model protein and the suchlike. Without proteins like that, an embryo cannot live or develop.
there are ‘tolerant’ genes
On the other hand, there are genes which, when lost or mutated, do not immediately result in the death of the carrier, but do make the individual weaker. There are many examples of this kind. Many hereditary diseases fall into this category, such as hemophilia (blood does not clot after an injury, which can cause the carrier to bleed to death). All the genes needed for sight will be in this group. If they are not functional, the embryo will develop, but the carrier is then blind.
I will call these genes tolerant genes; the organism can tolerate elimination of these genes, but is not ‘happy’ with it, has a (serious) handicap as a result. 
There are neutral genes
they are primarily genes which determine hair, colouring, markings, and such appearance-based characteristics, neutral genes.It is especially the turning on or off of the neutral genes, and the combinations there of, which cause the variety from which natural selection can choose, but that is covered extensively in chapter 13.
NOTICE that in this division, we are talking about viability and not about chances of survival. This is about whether or not a gene is necessary at all for an organism to be alive, not about how big its chances of survival are once it is alive. So, in very concrete terms: essential genes are all the genes whose functionality absolutely must be present for an organism to be born alive and be able to reproduce itself. In addition, there are many genes necessary to stay alive and to survive. Insofar as those genes are different from the genes necessary to be born alive and/or reproduce oneself, by definition they do not belong to the genes essential for life. Natural selection can for example easily select for neutral genes, or combinations thereof, which could make them essential to survive, but that is not what I mean here. Even if those neutral genes are essential in order to survive, they are still not essential for viability.
We get the following overview:
Essential genes 

gene loss of function means example
essential genes no viability Topoiosomerase
tolerant genes handicap but vaibility Hemofilie gen
neutral genes no consequenses for the viability Oogkleur
Table 1, the division of genes into categories

The line between the different categories will not always be clear in practice, just like any division or categorisation. There will always be borderline cases where the division is less clear, but that does not detract from the usefulness or even necessity of this distinction. It is actually much more dangerous to make no distinction at all, because principles which might apply to neutral genes will then be applied to essential genes without exception.
essential genes cannot evolve
Essential genes cannot evolve! As soon as a mutation in an essential gene is such that its (original) functionality is lost, that means that no viable or even living individual will be born! Perhaps essential genes in certain places which hardly make a significant contribution to the functionality (but maybe only to the structure) do permit mutations; however, as soon as mutations begin to affect the essence of the function, it goes wrong. In other words, essential genes cannot evolve at all! Essential genes are of course surrounded by the cliffs which lead to Dead Gene Valley. As soon as they lose their original function, while they are already mutating towards another function, at a certain point in time life is no longer possible for the embryo.
Take for example hemoglobin, which transports oxygen through the blood. This gene can never ever do anything other than transporting oxygen in the blood, or life cannot continue. The ‘function-acquiring’ mutation is not an option for essential genes.[16]
So, for clarity’s sake I will repeat it: 
Essential genes cannot evolve to another functionality. 
Perhaps (some) essential genes are susceptible to (multiple) mutations, but that can never go so far that the original function is lost. In this way, (at least) three mutant versions of hemoglobin are known, of which two make no difference and the third causes a serious illness, sickle-cell anemia (which will be discussed in chapter 11).In other words, genes which are essential to life live on the Mount of Isolation no matter what! Perhaps they have some freedom of movement there, but the cliffs are inevitably all around them (see figure 6).
This raises two questions. 
1. Then how did these genes originate? Were they at some point in time non-essential genes which became essential genes? Has evolution then in essence, meaning in the essential genes, stopped? 
2. Are the genes which fill the same functions in non-related species the same or different? If they are the same, there is no problem. Then all life must have received these genes from each other in some way. If they differ from each other and cannot be derived from each other, then there can have been no evolution between them.
In order to answer question 1, first an example is given in point 7 of a protein which cannot possibly have descended from predecessors. Next, in point 8, is a search to see whether or not more proteins like that exist. Question 2 is finally answered in point 9.
7.The Leapfrog protein is an essential protein which could not have evolved 
The Leapfrog protein (see paragraph 6.3) is a concrete example of an essential robot-protein, which cannot possibly originate from predecessors of that protein by ‘function-acquiring mutations’. It is an essential gene – without it there will be no viable individuals – which means that it lives on the Mount of Isolation and is surrounded by the sheer drop of non-functionality. And it cannot have originated from a non-essential predecessor. It is the Lone Ranger we seek…[17]
The Leapfrog protein is so specialised and dedicated to its task that it must fulfil several functions to be functional at all. These are those minimal functions:
1. It needs to attach itself to a strand of DNA on two sides.
2. It needs to be capable of cutting through that strand of DNA.
3. It needs to be able to hinge after cutting.
4. It needs to allow a second DNA strand inside or even to go and get it.
5. It needs to recognise that a strand of DNA is encircled.
6. In reaction to that recognition, it needs to be able to close.
7. It then needs to be able to glue the cut DNA back together again.
8. After that, it needs to be able to open without cutting the cut DNA again.
9. It needs to release or even remove the second strand of DNA.
10. It needs to recognise when the second DNA strand has disappeared.
11. It needs to release the first DNA strand.
The Leapfrog protein needs to be able to fulfil each of these functions. If one of them is missing, it means that it does not function at all. Each of these functions needs to be present from the beginning. Almost every one of these functions is a biochemical reaction which costs energy. For each of these functions, a specific combination of amino acids is required which is capable of fulfilling this function. If these combinations are not in very specific places in the protein, of course the protein also cannot function.
The Leapfrog protein is a hugely complex, specialised, dedicated, precise, integrated, adjusted robot-protein, with more than ten specific functions, all of which it must fulfil in order to be functional at all.
However, beyond this specialisation, there is another simple fact which shows that the Leapfrog protein could not have had predecessors: it needs to be at least big enough to encircle a strand of DNA! A hypothetical predecessor of the Leapfrog protein that was not capable of encircling a DNA strand would certainly not have that function at all, 100%! Even if many forms of the Leapfrog protein were to exist which could have been derived from each other by mutations, not a one would be able to function if it were not at least capable of encircling a strand of DNA. If that were not possible, it would have to release the cut strand of DNA in order to allow another DNA strand to pass through. That means that it is very much in doubt whether it can find that end that it released or that then any other loose end could be attached to it (there are always more than one of the same kind of protein active at the same time). Considering the loss of information, this can never be permitted. Thousands of mistakes would be made with every cell division, which simply means that no cell division is possible. Natural selection would send an organism which handles the DNA in such a destructive way directly to hell!
Graph 4 shows that the functionality (or complexity) is null up to the point in time that a strand of DNA can be encircled; from that point onwards. the functionality/complexity could (theoretically) increase.
Whichever way you look at it, the Leapfrog protein has no beginning. It has to be present all at once or it does not work. Because the Leapfrog protein is such a large protein, it has to be made up of many hundreds to even thousands of amino acids (I could not find the exact number anywhere). This ‘beginning’ could therefore also not possibly have originated ‘coincidentally’.

Graph 4the Leapfrog protein cannot have originated by ‘function-acquiring mutation’ (compare graphs at point 5)

In short, the Leapfrog protein did not evolve. The Leapfrog protein is our Lone Ranger. The Leapfrog protein shows that Darwin’s idea of evolution is a genetic impossibility:
If it could be demonstrated that any complex organ ( or gene! PMS) existed, which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down.Charles Darwin, The Origin of Species
point mutations cannot elongate proteins 
The above example, by the way, shows a serious lack in mutation in a surprising way: it actually cannot make proteins any longer than they already are! 
The Leapfrog protein (or a possible predecessor) can never have received its complex, specialised function all at once by sheer coincidence. The only alternative (apart from the problems discussed before) would be a step-by-step increase in the length of the arms. A too sudden arbitrary change would mean loss of function and condemnation by the Angel of Natural Selection. 
The point now is this: How can a protein become longer? Not by inserting base pairs, because in an insertion one base pair is added, which makes that entire code move over one base pair, and all information is lost (see chapter 4.4). And insertions do not happen in groups of three! Insertions, just like deletions of course, drop out. 
A point mutation, however, changes only an existing amino acid. The only way in which a protein would be able to grow longer is therefore by a few point mutations on a multiple of three base pairs, after the stop sign, which causes a new stop sign to arise. Afterwards, the original stop sign must change into an amino acid by mutation.
There are a few problems with this: 
· Is the space after the stop sign available for ‘growth’? It could be that the code for a new gene is located there. 
· Such an occurrence can take tens of thousands, if not millions of years, because a number of non-arbitrary mutations on specific locations are needed, which makes the chance of that happening extremely small! 
· Next, the Leapfrog protein does not benefit if this happens! The elongation of the arms would have to take place in the top of the C, in the middle of the C, and on the bottom of the C, so at several places in the middle of the protein sequence. That has to happen in such a way that the protein can still fold up well, not a single one of the functions that are present are endangered, and the C has grown a bit longer. Adding one or more arbitrary amino acids to the end of the protein sequence leads nowhere! 
This serious shortcoming on the part of Master-Crook Mutation means two things: 
1. There is another reason to understand that the Leapfrog protein could not have originated from more simple predecessors. 
2. Master-Crook Mutation needs to be written off as a mechanism for gene growth. Because of his volatile disposition, he cannot usefully elongate proteins. Once two functional parts are definitely established on a location about, say, 30 amino acids apart, he can no longer possibly put anything in between. The longer the arbitrary piece is that he sticks in somewhere by changing the stop codon, the more nonsense it will contain, and the greater the chance that it will become a useless protein. The smaller the piece he sticks in, the less probable it is that it occurs regularly (one arbitrary mutation is possible, but to have it repeatedly three or four times at specific locations with specific results is too much to ask). 
8. The greater part of the genes does not vary at all!
The important question now is whether Lone Ranger Leapfrog protein is a lonely exception, or whether there are more of that kind of genes, which are surrounded by precipices, genes to which no paths lead?
The answer is yes. Far from all genetic information is known even about humans, but there are probably many examples of this kind of protein to be found, which will be found in the coming years. That can be derived from an interesting fact from population genetics. 
Considerable variation is present in natural populations. At 45 percent of loci in plants there is more than one allele in the gene pool. [allele: alternate version of a gene (created by mutation)] Any given plant is likely to be heterozygous at about 15 percent of its loci. Levels of genetic variation in animals range from roughly 15% of loci having more than one allele (polymorphic)[18] in birds, to over 50% of loci being polymorphic in insects. Mammals and reptiles are polymorphic at about 20% of their loci - - amphibians and fish are polymorphic at around 30% of their loci. In most populations, there are enough loci and enough different alleles that every individual, identical twins excepted, has a unique combination of alleles.Chris Colby, The Talk.Origins Archive, Introduction to evolutionary biology.
About one-third of structural-gene loci are polymorfhic, and the average heterozygostity in a population over all loci sampled is about 10 percent. This means that scanning the genome in virtually any species would show that about 1 in every 10 loci is in heterozygous condition and that about one-third of all loci have two or more alleles segregating in any population.Genetic analysis, pp. 784.
In populations of the fruit fly Drosophila, the gene pool typically has two or more alleles for about 30% of the loci examined, and each fly is heterozygous at about 12% of its loci…
The extent of genetic variation in human populations, is comparable.Biology, Campbell, pp. 426.[19] 
No variation has been discovered in mammals in at least 67% (80% for Chris Colby, and 70% for Campbell) of the genes. I repeat: in mammals, in any case more than 65% of the genes show no variation. That is unbelievable! How is that possible? 



Figure 10. The biggest part of the genoom of each 

There are species which, according to scientists, have not changed at all in millions of years, such as for instance sharks. In those millions of years, a mutation has occurred often enough on every location in the genome. Humans, for instance, have 3 billion base pairs and there are 6 billion people, and on average there is probably 1 mutation in each person. Over a period of millions of years, that means that mutations have simply happened everywhere. But then why are two-thirds of the genes still the same? The answer is, of course: by selection! One amino acids sequence was chosen above another, was ‘more suitable’. Then, by selection, that sequence of amino acids was maintained. If mutations recurred that had the same effect, that was also so disadvantageous that either the individual could not live, or it could not survive.
But what does that tell us about the functioning of the proteins that belong to those two-thirds of the genes?[20]
That one single change in amino acids can have such far-reaching effects on the functioning of that protein that selection can take place for it. Once more, but slightly differently: one change in an amino acid already changes the functioning of that gene in such a drastic way that it can no longer fulfil its original function at all, or at the very least more than insufficiently. If a change in amino acids should almost not or barely influence the functioning of the protein, no selection could take place for it and then one amino acid sequence would not be chosen over another. Now that that does happen, that simply means that these genes do not permit any change at all. Their functioning is so specialised, so critical, so dependent on the exact sequence of amino acids, that they permit no change at all, because that would mean the loss of the entire function to such an extent that the carrier of the mutated gene cannot live or cannot survive.
These genes have natural variation because the Angel of Natural Selection is unfeeling. It pushes the protein off the cliff after one mutation that makes a difference. The protein dies immediately after one single alteration. The protein loses its entire functionality. And with the dead protein, the organism itself also dies before it is capable of passing on the mutated genes to the offspring. And that is why variation does not occur in those genes (as far as the amino acid sequence of the protein).
And guys, we are not talking about one single gene here, about a lone exception. No, 67%. More than half! The greater part! Bingo! 


Figure 11, Adoptive landscape of essential genes

Those proteins are prisoners of the Angel of Natural Selection. They have absolutely no freedom of movement. They are sitting on lonely, towering peaks without any connection to anywhere at all. Below the peak wait the dogs of King Entropy, and on top, the Angel of Natural Selection keeps them in seclusion. No variation. Not a step to the left or the right, or any of the hundred possible directions. No hidden path through a few fog banks. Not a single minimal infinitesimal change. They are grounded. They have to stay where they are. Master-Crook Mutation can do nothing. Every action he makes is immediately punished. His back is to the wall. In these non-variable genes, he apparently has no right to speak at all! This means that these gees could not have originated by a gradual accumulation of function changes. Or, in proper English: they cannot evolve and they did not evolve. They did not originate through evolution. Two-thirds of the genes do not evolve. 
Hey, Charles. Two-thirds of the genes do not evolve!
If there is no other mechanism for the sudden origin of genes, this in itself is sufficient to conclude that macro-evolution is a genetic impossibility. Molecular evolution concerns at most the rest of the genes, for which some things may be possible.
we have been misled by Master-Crook Mutation
It seems that Master-Crook Mutation has pulled the wool over our eyes! Not that he does not exist! Not that he is not ca[able of anything! But he has managed to sketch for us a friendly image of the protein landscape where everyone likes everyone and where proteins, already mutating, visit each other and change function and form, where a protein does get lost every once in a while, but is then kindly taken away by the Angel of Natural Selection to have tea with King Entropy. The harsh reality is evidently completely different. We will bring another charge against Master-Crook Mutation! 
there is still an alternative explanation 
There is still an alternative explanation for the non-variability of most gene, which, however, testifies just as strongly against the macro-evolution idea as the previous one. That alternative is that they do permit mutations, but that there simply has not been enough time for that to happen. Or in other words, in humanity’s case: the total human population descended fairly recently (say a few thousand years ago) from a human Adam and Eve, from whom we have thus received exact copies of their original genes. In that relatively short period of time, all the possible neutral mutations have not yet been able to spread throughout the entire world population. 
Still, in my opinion, this could only account for a part of the non-variability. Even in ten thousand years, mutations could occur in all locations over the whole genome. Perhaps these mutations did not spread throughout the entire world population, but if you looked around a bit, you should be able to find them all. That is apparently not the case. 80% of genes in humans are required to be the same. 
At the moment that it is evident that all the gene that are now non-variable do permit mutation to some degree, the fact that it is now not the case is, of course, just as final an argument against an evolution millions of years in length, as when it is evident that these genes do indeed not permit one single change in amino acid. For instance, sharks have been supposed not to have changed at all over millions of years. In that time, all the possible changes that make little to no difference should be criss-crossing the shark population, because one will never be selected over the other. Naturally, a certain gene can, by coincidence, disappear from the population entirely with a neutral mutation (because it is not passed on), but that cannot work for two-thirds of the genes after a few million years, because mutations occur again and again, at the same locations.[21] 
There are therefore two possibilities:
1. The proteins turn out to permit changes in amino acids. Then the species (and all life therefore) just has not existed as long as has been assumed. 
2. The proteins do not permit changes in amino acids, because one single change means the loss of the entire function. In that case, they could not have originated by ‘functional change’. They are surrounded on all sides by the precipices of loss of function. 
In practice, both will probably turn out to be true. The relationship between the two dos not matter. In one case, evolution did not happen. In the other case, evolution could not have happened! In the rest of this chapter, I will assume that neither one of the two possibilities is solely responsible for the non-variability of most genes, and that there are thus many genes which do not permit any change at all.
9.Essential genes can differ greatly between non-related species
One important question, which has been posed before, is this: do the genes differ (significantly) between non-related species. That question is important, because if the genes that do not allow any change at all are the same in non-related species, then that means that evolution between non-related species is possible after all.But, unfortunately, that is not the case. The genes are different. There are of course many genes which are not different, but it can be clear that a jellyfish does not have the genes that a human has, even though a number will correspond (both are made up of cells and have DNA, just to name a few).
An extremely interesting group of very essential genes, which will permit no or little change, but do differ greatly and cannot have been derived from each other, are the gender-determining genes. These genes are surrounded on all sides by the precipices of non-functionality, because they are essential in their own way: without them there is no gender (or at the most one, which is then usually not fertile) and therefore no reproduction. Then they have influence over tens or hundreds of other genes which determine the difference in gender. If the gender-determining gene has changed, all those other genes must change simultaneously, which is genetically impossible. Therefore, in practice they will permit very little change. And they differ between non-related species. The gender-determining gene in fruit flies is a so-called RNA-binding-cutting protein, and in humans it is a DNA-binding-translating protein. In chapter 15, I give an extensive description of these genes and of other gender-determining systems. 
non-related species are not descended from each other
The fact that essential genes cannot really change, combined with the fact that most genes do not permit any change at all, shows that in essence, in other words in those non-variable and essential genes, a species does not change. That means that it stays the same type. (Within that type, very diverse variation is possible and new variation can arise. See part II, chapters 13, 14, and 15.)
On the other hand, genes can differ greatly between non-related species, such as the gender-determining genes. These three facts thus show that non-related species are not descended from common ancestors:
Proteins can differ greatly between non-related species.There are therefore two possibilities: 
1. Essential genes cannot evolve past their own functionality 
2. Many (essential) protein do not vary at all. 
3. The proteins turn out to permit changes in amino acids. 


Figure 12.Each animal has (among other kinds) essential genes, which do not permit mutations (green), tolerant genes which result in a hereditary disease or handicap when lost or damaged (brown), and neutral genes which are by their very nature cause variation (red).

Cytochrome c differs between non-related speciesIn 38 species, research has been done on cytochrome c, and it turns out that each species has a different version of that protein. With humans and Rhesus monkeys, it is a difference of one amino acid, with horses twelve, kangaroos ten and baking yeast forty-five. Cytochrome c is a small protein of 104 amino acids, which plays a part in electron transport in mitochondria and can therefore be called essential: without it, the carrier cannot live. An interesting question is now: is cytochrome c one of the proteins which permits no change at all? The only way to find out 100% for sure would be to test each possibility within every species. That confronts practical problems. What can be said about cytochrome c, however, is that (even if one single change in amino acid might be possible) it cannot have evolved right through all the species and left each species with its ‘own’ version. And that is because of the teamwork of the genes.We have already discussed the fact that a protein often needs a key to function, or a keyhole and/or a kind of ID. Such a ‘password’ has to link up precisely with other proteins with which it works. One mutation in cytochrome c (to the extent that it does not immediately incapacitate the protein) means that simultaneously, various other protein must mutate in such a way that all the keys and locks still fit! Or, in other words, the entire metabolic pathway in which cytochrome c functions has to be reprogrammed by simultaneous, arbitrary mutations, which are attuned to each other! Donald Voet writes in Biochemistry:Cytochrome c is a rather small protein that, in carrying out its biological function, must interact with large protein complexes over much of its surface area. Any mutational change to cytoscrome c will, most likely, affect these interactions unless, of course, the complexes simultaneously mutate to accommodate the change, a very unlikely occurrence. (Italics by PMS) Biochemistry, pp. 128.If you then take the frequency of mutation which follows from that into account, it follows that, in the arbitrary practice of life, that is impossible. In humans, each gene has a chance of mutation somewhere between 10-4 and 10-9. The chance that two mutations happen simultaneously, one in cytochrome c and the other in the larger protein complex with which it has to react is an average of 10-4 x 10-9 = 10-13.The chance that the mutation in cytochrome c (104 amino acids in humans) is on the location where the interaction with the larger protein is, say, 1 in 10; in the larger protein, say, 2,000 amino acids, it is 1 in 200. This makes the total chance approximately 1 in 1017.If a third mutation is necessary to let the keys fit, the total chance is about 1 in 1026. So many living creatures have not even existed in 5 billion years!A contradiction for this could be this: you should not calculate the chance of a certain coincidental occurrence afterwards. If you were to throw a series of 100 dice, the chance afterwards if have thrown it is always 6100, but that particular series still resulted. Such a ‘calculation of chances’ therefore no longer matters.Still, it does matter. In the series of dice, every possibility is good. If only half of the possibilities were good and you throw a good series, the chance of that was 50%. If only one combination was good and you throw that, the chances were, even afterwards, 6100. In this case (and in all other cases in which proteins react with each other, in other words most of the time!) only one, maybe two, maybe three specific countermutations are possible at the exact moment that the other mutations also happen, because otherwise the keys would no longer fit. Even now, beforehand, the chance that three simultaneous mutations in cytochrome c & co. happen in such a way that the keys continue to fit is 1 in 1026, or if there are perhaps ten or one hundred possibilities for permanent keys that fit, 1 in 1024. The precisely attuned teamwork of the genes requires that an entire, specific, non-damaging path is travelled. If evolutionists claim that such paths have been travelled, it is quite possible to ask yourself ‘afterwards’ if that was actually possible.The fact that a protein like cytochrome c differs between non-related species, but is the same within one species, shows that the non-related species do not have a common ancestry. The point of the different versions of cytochrome c is that they all do the same thing: transport electrons. Natural selection can thus never choose one version over another, because they all do exactly the same thing. A term has also been thought up for that: neutral drift. But it is then strange that different versions of cytochrome c are not also found within the same species (such as perhaps the sharks, which have not changed in millions of years)! It could be called extraordinarily coincidental, if not to say miraculous, that these neutral changes always and only take place around the diverging of two species. What does that indicate? Either the non-related species have no common ancestry and each species received their own variant of cytochrome c, which then theoretically (or by genetic manipulation) could change. Or cytochrome c, in combination with the protein with which it reacts, does not permit any mutations, which means that the non-related species do not have a common ancestry. (This was concluded earlier, but now we see it confirmed in practice.) 
10.The Evolution Mountain Range
In the immeasurable plains of non-functional protein country, there is a mountain range with all sorts of peaks and paths and plains and everything we would want it to have. There, Master-Crook Mutation can do what he wants to. There he works together with the Angel of Natural Selection to create the most beautiful, well-formed proteins. Above the mist which divides the peaks of those mountains, called the Evolution Mountain Range, from the realm of the dead, the sun shines, the grass is green, it is lovely to linger. And yet, inevitably, the distance to another mountain is immeasurably great. If you don’t think about those other lonely peaks, you can dream that the life of the proteins is like this everywhere, like here on the Evolution Mountain Range, where the Angel of Natural Selection has built its castle. He even gives guided tours to tourists and Master-Crook Mutation assures everyone that it is like this everywhere and that there is a path from the Evolution Mountain Range to every other protein and that there are so many proteins that they cannot see all the paths anyway and that the mist which hangs around the border with the kingdom of the dead hides secret passageways and underground tunnels, along which mutating proteins can go to avoid the inexorable clutches of King Entropy. And he says to the visitors, “That can’t be true, can it? That there are no paths anywhere? Look, here one is, right in front of me! Did you see it?’, and everyone laughs. 
Because Master-Crook Mutation is so good at his trade and because the reality of proteins is so complex and therefore he probably knows what he’s doing, and... because we want it to be true, that’s why we believe him.
11. A bone to pick with E. coli.
We still have a bone to pick with E. coli. (see the beginning of paragraph 6.4.2), concerning the function-altering mutation. I will line up why it is not a case of adoption. 
a) It is a case of mild functional change, not of adoption of a new function, or in other words, this is at most some manoeuvring on a remote plateau.
b) A cross-section of the adoptive landscape of the protein looks like this:

Figure 13. mutation sensitivity for the ebg gene of E. coli(a cross-section of the adoptive mountain)
c) There were three non-arbitrary (because they were carried out by B. Hall) mutations necessary to bring about the change in the protein. If this were to happen in nature, the protein would be a dead protein after one change and the selection pressure would have disappeared. But it is possible that Fool Coincidence could have managed to fool King Entropy...
d) Because no clear function was known for that gene, could it have been a duplicated lac-gene that was already dead?
e) There was absolutely no question of metabolic adoption, because the regulator gene was emphatically eliminated. For metabolic adoption (which means: not eliminated, but regulation attuned to the new function), many subsequent mutations would be necessary, all without selection pressure, and therefore, the gene would be under the power of King Entropy.
f) Such a suspicious way of ‘changing function’ cannot be representative of the large-scale structural changes necessary for macro-evolution or gene growth. This is ‘messing about in the genetic margins’ of a species. This is not a mechanism by which the genes for Darwin’s most primitive eye will originate.
g) Because bacteria and moulds are exceptionally simple organisms, the possibilities for the origins of derivative proteins are greater than in higher plants and animals.
Conclusion:
It could be possible that, in living nature, a gene with a derivative function does originate in this way, which has survival chance under high selection pressure. Still, this cannot explain the origins of dedicated, specialised, precisely regulated (groups of) genes working together.
6.4.3 Metabolic adoption
So far, we have only discussed functional adoption through gradual change, which means the origin of some genes and protein improvement. We have seen that, in some cases, a mild functional change is possible, but that protein specialisation in many cases means that there is no path at all that they can walk to have descended from predecessors, or to ‘grow’ to another function. Metabolic adoption actually comes right on top of functional adoption. If functional change takes place, metabolic change must take place simultaneously. A multiple of functional adoption is necessary for metabolic adoption, because this always involves several genes. If functional adoption is not possible, metabolic adoption, the origins of new groups of co-operating genes which are dependent on each other, a complete impossibility! The twelve genes which are necessary to make a cell light-sensitive in Darwin’s most primitive eye are an example of that. The ‘leap’ to the function of a single protein has already been proven to be too big in a number of cases, let alone the jump to twelve co-operating genes.
there is a certain tolerance
enes permit mutations which influence their function, or in other words that there is a plateau on which they can move around, shows that there is not only a refined degree of attunement between all genes, but also a certain tolerance. The problem with evolutionists is that they raise this kind of exceptions to the level of a rule of the vehicle that brought evolution in our country. 
All the parts in the engine of my automobile together form just such a refined mechanism, in tune with each other, as gene teamwork. Small alterations in the functioning of engine parts do not necessarily have to mean that the engine no longer runs at all, although it is possible. That depends on how important that part is and how drastic the alteration is. However, if the alterations accumulate, in the long run the engine will perform less well, until at a certain point in time it no longer works. Small alterations which do not immediately immobilise the entire functioning exist by the grace of an already working, well-tuned whole.
Now an engine is not a living organism and is made up not of twenty but of many more parts (a protein is not actually alive either, it is only a molecule). But this is about understanding the comparison with the term tolerance. However, if the small alterations accumulate, in the long run, such a ‘worn-out’, no longer well-tuned whole that it is question of a degenerated species!
However, it can be clear meanwhile that this kind of ‘fraud’ in the DNA by mutations is absolutely insufficient to explain structural gene growth, adoption and evolution.
To propose and argue that mutations even in tandem with ‘natural selection’ are the root-causes for 6,000,000 viable, enormously complex species, is to mock logic, deny the weight of evidence, and reject the fundamentals of mathematical probability.I.L. Cohen, Darwin was wrong: A study in probabilities, pp. 81.(quoted from Acces Research Netwerk at www.arn.org) 
another amino letter game 
A parallel or comparison which goes very well with base pair and amino acid changes is our amino letter game. There are also about 20 letters and the relation between useful and useless combinations is very much to the benefit of the amino letters. In order to approach reality more closely, we will make it more difficult. This is the sentence:
mutationsareinnowaycapableofcreatingnewdedicatedcomplexcooperatingpresciselyregu
latedgenes.everythingaftertheperiodisactuallynonsenseabcdnonsensenonsintestte.stow
dicgigclkgnmiadgyncli
But now, on the basis of the table in chapter 4.4 with the ‘genetic’ code, we get a nice strand of DNA:
[ATG TAC TGG GCG TGG GGC CGC ACA ACG GGG CAT TCC CTT TTT GAA 
CGA AGA TCT CGG AGT ATT AGG AAA CGG GTG GGC CAT ACG CGG GGT 
TCT ACT TGG GCG GCC TGG TCA GGC AGA TAC GTG AGG TGG TTA CGA 
GAG AGG GTT GGG CAT AAT CGC ATA CTT ATG TTT AAA CGT ATT ACA 
ACA GCT ATG AGG TCT GTT CGC CCT ATA AGA TCT AAT CGT AGC GCT 
TAC GTT ATC CGG TAT CCT GGT GAG GAG CGA CCT AGG GAG TAC AAA 
CGC CGG CCC AAT AGG GAA CGT TCA CGG AGT TGG AAT CTC CGT TCC 
CTT TCA TGG ACC TGG GCT GCA TCC TGA AGC TAG CGC CTC AGA CTG 
CCA TCG GTA GTC GGG CAC CTA CGG CTC AAA GAA CTA ACG TTC GCG 
CCA GTG GAT GCA GTC AAC AGC ACA CTC TGA CGG GTG GGG CTA
According to the principle of arbitrary-mutations-plus-non-arbitrary-selection, one base pair can be changed each time. (One base pair can also be removed or added, but that will definitely not result in anything.) If that change results in a ‘good’ English sentence, which my publisher would not correct if I had written it here (imagining the spaces), then that means that the sentence is still ‘functional’ and can be selected. In this way, a ‘path’ needs to be created from this sentence (or ‘peak’) to an arbitrary different sentence (or ‘peak’) which has a totally different ‘function’, so it says something completely different than what it now says. That sentence must be specialised in the same way and as dedicated as this first sentence right up to the period: every word has to contribute to the meaning of the sentence. Other than that, the s can be used for the z and the v for the w (because there are only 20 letters; this only gives more possibilities to find a path) and we will not be too picky about spelling.
The reader will discover that such a ‘protein’ is not very tolerant of ‘mutations’, or in other words: there is not much to select.
That doesn’t make this game much fun, so let’s just assume that this protein is not essential and that is does not work precisely with other genes and therefore can contain as many grammar mistakes as is possible! However, with this qualification: my publisher has to be able to read the sentence and correct every grammar mistake so that he ‘understands’ what it says (in the co-operation of proteins, they also have to ‘understand’ each other or they cannot work together).
The reader will notice that there may be some variation possible now, but that changing it into another functional sentence does not work. And that while there are hundreds or thousands of possible sentences with about one hundred letters, many more than there are useful proteins with 100 amino acids! How is that possible? Because the number of useless combinations of letters is infinitely greater than the useful ones, so that the above sentence is ‘surrounded’ by precipices of uselessness and ‘dead sentences’, into which it falls one a few ‘mutations’ accumulate.
6.5 Conclusions 
Master-Crook Mutation is not capable of causing the structural gene growth and adoption necessary for macro-evolution. Perhaps his family is capable of it, or that he can make beautiful new robot-proteins in co-operation with his family. That is also the subject of the next chapter. 
List of difficult words:
structural gene A gene that codes for a protein.
regulator gene A gene that regulates a structural gene, turns it on and off.
dead gene A gene that no longer codes for a protein or fulfils a useful function.
protein sequence The sequence of amino acids in a certain protein.
metabolism the biochemical process in which proteins and other molecules work on and with each other.
adoption Taking up or adopting new genes into the genome of an organism or even a species, which essentially contributes to the functioning of the organism, so that gene growth and an increase in complexity is possible.
functional adoption The adoption by a structural gene of a new function, different from the old, by any mechanism. In practice, this means a change in the DNA code for the protein.
metabolic adoption Taking up or adopting a structural gene that has undergone functional adoption, including the whole gamut of regulating genes, into the gene teamwork. Regulator genes, promotors and repressors can be involved in that, as can necessary changes further up the metabolic ladder.
gradual adoption Functional and/or metabolic adoption by means of accumulative mutations which continually minimally changed the original function. By gradual adoption, a gene grows, as it were, to a new function it did not have at first.
leaping adoption Adoption in one generation of one or more genes with new function.
adoptive landscape Schematic representation of the lower boundary at which a protein has lost its functionality completely, becomes a dead gene, and/or has a connection above the selection border to another functional protein.
selection border The border at which a protein becomes a dead protein, which means that there is no longer (indirect) selection pressure on the protein sequence.
polymorphic There are multiple alleles of one gene in a population.
locus, loci The exact location of a gene on a chromosome.

Micromutations do occur, but the theory that these alone can account for evolutionary change is either falsified, or else it is an unfalsifiable, hence metaphysical theory. I suppose that nobody will deny that it is a great misfortune if an entire branch of science becomes addicted to a false theory.But this is what has happened in biology; ...I believe that one day the Darwinian myth will be ranked the greatest deceit in the history of science. When this happens many people will pose the question: How did this ever happen? …S.Lovtrup, Darwinism: The refutation of a myth, pp. 422.
(quoted from Acces Research Netwerk at www.arn.org)




[1] "Evolution has no direction, there is no goal, it is absolutely arbitrary.” is an often heard objection. The fact remains, however, that there was an increase in complexity from amoeba to human and that should still be the case. Whether that is arbitrary (as evolutionists say) or towards a goal (which they dispute) makes no difference at all.
[2] For clarity’s sake. There is an increase in genes vertically and horizontally. The vertical increase is in fact a mutant, a diverted allele, coming into being from an existing gene. Within a population, one individual has this allele, another has that allele of the same gene, or better, on the same locus. What I call gene growth is an increase in the number of genes within the individual, from 10,000 to 10,001. Horizontally, in other words. 
[3] I had announced my intention earlier to leave bacteria out of consideration, because their reproductive system and system of variation is totally different from that in plants or animals. However, this is about gene regulation. That is comparable, with the difference that everything is much more complex in animals, because bacteria do not have a nucleus, and in bacteria, everything happens within one cell, whereas in animals this takes place in different organs. The treatment of such an animal system would become too extensive and complicated. However, the principle of regulation of genes remains the same. 
[4] It seems as if someone... 
[5] Each human cell contains 2 meters of DNA, distributed over 46 chromosomes. This seems ‘short’, but on a molecular level, it is ‘astronomically’ long.
[6] The ‘power’ and the ‘Creator’ Darwin talks about are none other than his power: Natural Selection. Maybe it is even meant ironically.
[7] a bacteria which in often used in laboratories and often occurs in the intestines.
[8] In fact, there is a difference between a dead gene and a dead protein. A dead gene is a piece of DNA which used to code for a protein, but is so damaged by mutations that it no longer even makes a protein. A dead protein is a protein which no longer has any function. A dead protein in that sense always has a living gene behind it. This distinction is not really important for the rest of the story, so I do not make it in the text. A ‘dead gene’ may be considered, in the rest of the story, as a live gene (which codes for a protein) with a dead protein (which no longer has a function). The word ‘pseudo-genes’ is also used in this context..
[9] At least, not double. Most genes occur diploid, i.e. in pairs. As a result, it could happen that one of the two genes is defective, whereas the other ‘still works’. However, it is also possible that two good genes are still necessary, and that for one gene of the pair to become defective would be sufficient to prevent the possibility of viable individuals. 
[10] Of course, proteins do not mutate, genes do. Just to prevent having to explain it every time, I call them ‘mutating proteins’ in practice, it is the protein of a gene which is passed on to each generation and continues to mutate further.
[11] Selection does not happen directly for the amino acid sequence of a protein. Selection happens for individuals in a certain environment, or for 'gene frequencies', as that is called. Furthermore, detrimental genes can ‘hitch a ride’ with beneficial genes themselves, because they are very close to each other in the DNA. However, indirectly, a certain amino acid sequence of a gene is chosen over another sequence, if selection occurs. This (indirect) selection thus disappears as soon as the function is lost. 
[12] In addition, even in a population of five billion people, it would take a few million years before there is even one gene which has for instance undergone ten mutations, because after all each person has on average one new mutation, but the chance that that same gene mutates in a subsequent generation is very small. Because of this, (in humans) even in large numbers, it would take millions of years before there were any genes at all which had undergone more than ten mutations. 
[13] 300 amino acids times 3 base pairs times 3 other bases = 2700. Because of the way in which the genetic code is structured, in the worst case there is only one chance and in the best case 3 chances to regain the same amino acid. 
[14] It is possible for a protein to have a bit more of a chance to get its original function back, as long as it lands somewhere on the plateau. This kind of mutations towards the original state, or ‘revertants’, will mostly take place in the laboratory, where an artificially high frequency of mutation takes place and an artificially high degree of selection is applied.
[15] By gradual function-acquiring mutations. The alternative, change of function in leaps and bounds, will be covered in the next chapter.
[16] In some cases, because genes occur in pairs, one half could go astray while the other remains functioning. When such a lethal allele becomes homozygotic, the carrier dies as an embryo (for instance). It is estimated that every human has about five such genes. Still, these genes do not actually ‘evolve’, because the other half ‘cannot’ accompany it. It is as it were chained to the wall by one leg, in contrast to other genes, which have to be homozygotic and therefore are chained to the wall by both legs.
[17] There are more Leapfrog proteins, each with their own specific characteristic. This actually applies to the whole group.
[18] Polymorphic thus means that for one gene, or on one locus, many alleles occur within a population with the various individuals.
[19] Because of the importance of these figures, I have quoted three sources. It can be clear that the facts are reliable enough, even though they do not correspond exactly.
[20] Genes can differ even as they still code for the same protein. This is due to the structure of the genetic code, which neutralises some mutations. On that location, the same amino acid is then ‘indicated’ after all. It is important, of course, whether the proteins differ, not whether the genes differ.
[21] By the way, an interesting test comes from this matter which can find out how long life has existed. Because one amino acid can be indicated by up to six codons, and these codons can often change into another already from one change in the third base pair, there must be an enormous amount of this sort of neutral mutations in the DNA, if life is old, especially in species which, according to the evolution theory, have not changed in a long time. It is first necessary to have information from a large number of very widely varying individuals, the knowledge of the present frequency of mutation (and not the frequency which was calculated on the basis of the evolution concept), and the idea that the frequency of mutation has always been constant.

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