The proponents of the evolution theory speak

A cosmic drama is in progress, a drama of biological and biochemical nature. This drama contains various players, and before we can understand the game, we have to know the actors. I would like to introduce them now, but I will do so through the voices of the researchers of the biocosmic drama, so that it will be clear that they are not my own creation! I will do so extensively, so that we can form an accurate picture of the actors, their backgrounds, and their motives. As we do this, the nature and extent of the biocosmic drama will unfold before our eyes, but the true high point will not be enacted until the next act.

Below are my sources (for this chapter). The order is somewhat deliberate. The further down the list, the more thorough and to some extent more reliable the material in the source is. The Talk.Origins Archive is, in that sense, the most superficial source, the biochemistry book the most thorough. The increase in reliability is due to the fact that the theory must be tested according to the laws of biochemistry and be in agreement with them, or it is a fantasy.
I provide the quotes with comments in some places, without discussing it in depth, because that will take place in the next chapter.

A. The Talk.Origins Archive
This is the most extensive Internet site about evolution, with a large collection of articles, which often viciously attack those with different opinions. In comparison with the other sources, it is somewhat less supported, and there are quite a few strong statements being made. However, it is an often-visited site and goes deeper than the material you get at school. The address is: http://www.talkorigins.org/

B.  Michael Denton’s Evolution: A theory in crisis, 1985
A molecular biologist who dared to openly criticize the evolution theory by claiming in his book that evolution on a large scale no longer happens, and suggests more of a typological model of species. Because he is, in that sense, difficult to present as a proponent of evolution, I do not quote him very much. However, his remarks are very important!

C. Richard Dawkins with his books The blind watchmaker and Climbing mount improbable.
He is a very popular author whose books have been translated into many languages. He is more Catholic than the Pope (read: more evolutionary than Darwin), because for him it is not the individual or even the species that tries to survive, but the DNA, the genes, which to that end use the individuals and the species as ‘survival machines’.

D.  Niles Eldredge and Stephen Jay Gould introduced the theory of Punctuated Equilibrium, which is nowadays accepted by everyone, despite the fact that they oppose Darwin (wrongly according to some, such as Dawkins). In the December 1996 issue of Earth Magazine, Eldredge wrote an article with the title What drives evolution, from which I quote. This therefore gives a very recent view of the present state of affairs.

E.   Christian de Duve, De levende cel (The living cell), a publication of Natuur & Techniek (Nature & Technology).
Natuur & Techniek is a popular (popular-) science monthly magazine and in that sense important. Besides the magazine, Natuur & Techniek publishes many books, including this one by Christian de Duve. It is the only Dutch source.

Textbooks
F.   Biology, N.K.Wessells (Stanford University) and J.L. Hopson, 1988
A large volume with a distinct evolutionist slant. A textbook for biology students.

G.  An introduction to genetic analysis, A.J.F. Griffiths (University of British Columbia), J.H. Miller (University of California, Los Angelos), D.T. Suzuki (University of British Colombia), R.C. Lewontin (Harvard University), W.M. Gelbart (Harvard University), 1996
A comprehensive textbook (also quite large) about everything about genetics. Several passages about evolution.

H.  Principles of cell and molecular biology, L.J. Kleinsmith (University of Michigan), V.M. Kish (University of Richmond), 1995
Another large volume all about cells and their biochemical reactions. Contains only a few paragraphs about evolution.

I.   Biochemistry, D. Voet (University of Pennsylvania), J.G. Voet (Swarthmore College), 1995
Large volume. Not much about evolution. A lot of proteins and biochemistry

5.1     The actors are introduced
It is now time to introduce the actors:

a. King Entropy: nothing useful originates through coincidence (alone)
The first actor is King Entropy. He ensures that nothing useful originates through coincidence (alone). Listen:

A protein molecule is made of a large number of parts arranged in a very special way. The number of possible ways in which those parts could have been arranged is exceedingly large. In the case of a protein molecule we can actually calculate that large number. Isaac Asimov did it for the particular protein hemoglobin, and called it the Hemoglobin Number. It has 190 zeros. That is the number of ways of rearranging the bits of hemoglobin such that the result would not be hemoglobin. In the case of the eye we can't do the equivalent calculation without fabricating lots of assumptions, but we can intuitively see that it is going to come to another stupefyingly large number.Richard Dawkins, Climbing mount improbable.

The chance that one protein (‘polypeptide’ was the original word, which means the same thing, PmS), which is composed of 100 amino acids, would originate through coincidence, is 10^-130. Don’t try to imagine this number or to convert it into familiar units. Simply forget the idea of making proteins by chance. Even if the entire world population helped you by working day and night with the unbelievable speed of one million proteins per second without ever making the same protein twice, it would still take them 10¹⁰⁷ years
(5,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,
000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000 times the estimated age of the universe!) to produce all the possible combinations out of thin air.
Enough about this, it is quite clear.
Christian de Duve, De levende cel (The living cell), part 2.

King Entropy is the king of disorder, the emperor of chaos. King Entropy ensures that disorder always triumphs over order. Take a container with 100 white balls on the bottom and 100 red balls on top, and shake it.  King Entropy ensures that the balls will always be mixed and will never return to their original division, no matter how long they are shaken. King Entropy laughs at coincidence. How big is the chance that the red and white balls will become separated again as they were in the beginning? Well, each ball can take one of 200 positions. The chance that the first ball is in the right place is 100 in 200, the chance for the second ball is 99 in 199, the third 98 in 198 and so on. The end result is a very small number. The chance is very small. But there is a chance. So there is hope! If you just shake it long enough, it could happen eventually. Well, in theory it could, but in practice it doesn’t work. The chance of a coincidentally ordered arrangement is so astronomically tiny that it is unrealistic to take it into account in practice. And that is the work of King Entropy.

Figure1: A nice Job for King Entropy: An orderly tray of balls

Because why do the balls get mixed together? At the start, there are more red balls in one half than in the other. Is balls start moving around, more red balls from one half will move to the other half than vice versa (in the beginning none at all, of course). But suppose that there are now twice as many red balls in one half than in the other half. If it is then arbitrarily shaken, twice as many red balls will move downwards as from the bottom to the top. King Entropy ensures that the balls are always divided somewhere around 50%. Only with very small numbers can it happen that Fool Coincidence outwits King Entropy. Why is King Entropy such a powerful ruler? That is because the chance that the order is broken down is many times higher than the chance that the order is built up.

Figure 2: results of a simulation of the average distribution of red and white balls in a tray

In figure 2, you can see how that works out with 100 red and 100 white balls. The Y-axis shows how many white balls are on the bottom. at the start there were 100. The X-axis shows the number of times one ball goes from the bottom to the top. You can see that in the beginning, order disappears very rapidly, and after about 100 changes, hovers around 50%. Every once in a long while, the distribution rises above 60%. If you have a lot of patience and calculate this several thousand times, you might see it reach 70% once, but you will never make 75%, let alone the original 100%. The more balls involved, the less fluctuation. With 1000 balls of each color, you won’t even rise above a distribution of 55%!

King Entropy says, simply: highly specialized proteins cannot originate by themselves, I take care of that. If I put together a protein, it is always a gray, average, useless protein

b.Master Mutation: variation originates through mutation?
Master Mutation is not unknown to us. We have actually gotten to know him already. But Master Mutation has played a prank on us, which has fooled almost everyone.

Taken as a whole, hereditary changes originate almost without exception through alterations of genes: mutations.
Christian de Duve, De levende cel (The living cell),  part 2.

Mutation is a change in a gene. These changes are the source of new genetic variation. Natural selection operates on this variation.
Chris Colby, The Talk.Origins Archive, Introduction to evolutionary biology.

Evolution by natural selection could not be faster than the mutation rate, for mutation is, ultimately, the only way in which new variation enters the species. All that natural selection can do is accept certain new variations, and reject others.
Richard Dawkins, The blind watchmaker.

Mutation is a major source of genetic variation and serves as the raw material for evolution.Biology, pp. 1029.

What is the prank that Master Mutation has played on us? This: He is capable of making us believe that he is the one who causes variation. He doesn’t do that at all. He only manipulates. The process and mechanisms of natural variation, especially recombination, ensure that variation exists! Master Mutation manipulates himself in this system for variation, and because he talks so much, we have all begun to think that variation is caused by him. Rather, there are all sorts of biological and chemical processes that try to prevent Master Mutation from Carrying out his pranks in the DNA. There is not one single genetic mechanism that introduces, regulates or controls Mutation. Master Mutation is a burglar, who uses dangerous radiation or harmful substances to do his work. Master Mutation is a crook. And he now claims to be the owner of the House of the (infinite) Variation! From now on, we will call him Master Crook Mutation.

c.The true face of Master Crook Mutation: mutations are mistakes
The cellular machinery that copies DNA sometimes makes mistakes. These mistakes alter the sequence of a gene. This is called a mutation.
Most mutations that have any phenotypic effect are damaging. Mutations that result in amino acid substitutions can change the shape of a protein, potentially changing or eliminating its function. This can lead to inadequacies in biochemical pathways or interfere with the process of development.
Chris Colby, The Talk.Origins Archive, Introduction to evolutionary biology

Mistakes and accidents are the source of variability, which is as vitally important as the exact rendering^[1] , given it remains within acceptable limits.
Christian de Duve, De levende cel (The living cell),  part 2

Many mutations in the genetic information are damaging to the organism, leading to a competitive disadvantage or to death(…..). Occasionally, however, a genetic alteration lends some survival advantage to the organism. ^[2]Biology, Wessels & Hopson

The true nature of Master Mutation is, of course, difficult to deny.

d.Fool Coincidence: mutations appear coincidentally, arbitrarily, at random
Natural selection, the blind, unconscious, automatic process which Darwin discovered, and which we now know is the explanation for the existence and apparently purposeful form of life, has no purpose in mind. It has no mind and no mind’s eye. It does not plan for the future. It has no vision, no foresight, no sight at all. If it can be said to play the role of watchmaker in nature, it is the blind watchmaker.
Richard Dawkins, The blind watchmaker

One fundamental characteristic of mutations is that they take place completely by coincidence.
Christian de Duve, De levende cel (The living cell),  part 2

Master Crook Mutation and King Entropy are friends! Both of them harness Fool Coincidence to their purpose.

e.The Angel of Natural Selection: non-random selection selects certain genes
The process of evolution can be summarized in three sentences: Genes mutate. [gene: a hereditary unit] Individuals are selected. Populations evolve.
Chris Colby The Talk.Origins Archive, Introduction to evolutionary biology.

Random mutation + non-random selection = evolution
Richard Dawkins, The blind watchmaker

Ultimately, Darwin's theory implied that all evolution had come about by the interactions of two basic processes, random mutation and natural selection, and it meant that the ends arrived at were entirely the result of a succession of chance events. Evolution by natural selection is therefore, in essence, strictly analogous to problem solving by trial and error, and it leads to the immense claim that all the design in the biosphere is ultimately the fortuitous outcome of an entirely blind random process - a giant lottery.
Michael Denton, Evolution: a theory in crisis

There is a familiar, and I have to say rather irritating, confusion of natural selection with ‘randomness’. Mutation is random; natural selection is the very opposite of random.
Richard Dawkins, The blind watchmaker.
(Very strong remark! I come back to this extensively in chapter 6)

The game has countless variations and its progress is so unpredictable and variable that it goes beyond any understanding, natural or artificial. And yet, the rules of the game are extremely simple and can be summarized in three terms: exact rendering, variability, and selection.
…
What changes randomness into order is natural selection: every genetic change which increases the individual’s chances of survival – and more particularly of producing offspring – will be preserved at the cost of changes which do not increase these chances.Christian de Duve, De levende cel (The living cell),  part 2.

Master Crook Mutation has an acquaintance: the Angel of Natural Selection. The relationship between the two is not completely clear. Is the Angel of Natural Selection Master Crook Mutation’s accomplice? A demon? Or is she a saving angel, who relieves Master Crook Mutation of his bad reputation? Is she Master Crook Mutation’s guardian angel, or the guardian angel of the evolving species? Is the Angel of Natural Selection innocence itself, and is she too manipulated and abused by Master Crook Mutation? Our biocosmic drama will have to reveal the nature of the Angel of Natural Selection. Is she a Guardian Angel, an Angel of Salvation, an Angel of Death?

f. Insertion: he creates new, in this case ‘better’ genes
Only a very small percentage of mutations are beneficial. An allele that conferred a one percent increase in fitness only has a two percent chance of fixing (= to spread throughout the complete population, PMS). The probability of fixation of beneficial type of mutant is boosted by recurrent mutation. The beneficial mutant may be lost several times, but eventually it will arise and stick in a population. And, most importantly, even though "good" mutations happen much less frequently than "bad" ones, organisms with "good" mutations thrive while organisms with "bad" ones die out.
Chris Colby, The Talk.Origins Archive, Introduction to evolutionary biology.

The gain-of-Function Mutations
Because mutation events introduce random genetic changes, most of the time they result  in loss of function. The mutation events are like bullets being fired at a complex machine; most of the time they will inactivate it.^[3] However, it is conceivable that in rare cases a bullet will strike the machine in such a way that it produces some new function. So it is with mutation events; sometimes the random change by pure chance confers some new function on the gene. In a heterozygote the new function will be expressed, and therefore the gain-of-function mutation most likely will act like a dominant allele and produce some kind of new phenotype. ^[4]
Genetic analysis, pp. 186.

Figure 3, Null loss of function(a.), leaky loss of function (b.) and gain of function (c.) of a gene through mutations, as presented by Genetic Analysis pp. 187.

Mutation creates the new alleles that are a major source of genetic variation.
Biology, pp. 1027.

This is what it is about. These are the stakes of the game. This is where Master Crook Mutation wants us to be: he can make ‘better’ alleles. He is a protein-improver. And by an accumulation of  such ‘good’ alterations, he causes an increase in complexity and macroevolution, ...which is after all also how we originated. He doesn’t only have bad sides, there is good in him. The Angel of Natural Selection brings out the good in him. This is also why we don’t want to lose Master Crook Mutation: we need him. But the question is, is this true? Isn’t this a lie he thought up to save his doomed skin and not be rejected by us? Is Master Crook Mutation, in co-operation with the Angel of Natural Selection, trying to dethrone King Entropy? Is that what he wants? Can he do it? Are they capable of it? Or is he actually in cahoots with King Entropy.

g. Confusion: there are several levels of evolution
Microevolution can be studied directly. Macroevolution cannot. Macroevolution is studied by examining patterns in biological populations and groups of related organisms and inferring process from pattern. Given the observation of microevolution and the knowledge that the earth is billions of years old -- macroevolution could be postulated.
Chris Colby, The Talk.Origins Archive, Introduction to evolutionary biology.

Though natural selection remains the central shaper of adaptive evolutionary change, biologists now realize that the evolutionary process goes on at different scales at more than one level: on the molecular level within organisms as well as on the more familiar level of gene frequencies in natural populations.
….
Rather than assuming that the small-scale changes necessarily add up, inevitably, to large-scale change as the geologic ages roll, many of us now see that evolution is a hierarchical process – and that what happens at one level.need not specify what goes on at the next higher level.
Niles Eldredge, What drives evolution, Earth magazine, Dec. ‘96.

Macroevolutionary events include alterations in basic body design, such as the acquisition of a closed circulatory system in animals to allow larger body size or of stomata and guard cells in plants to control gas exchange in leaves. Alternatively, macroevolution may involve major changes in physiology, such as the evolution of amphibians from air-breathing fish and of vascular plants from nonvascular ones. Or there may be large-scale changes within a taxonomic group, such as the transition from foreleg to wing in the reptile-bird lineage and the transition from primitive, simple flowers such as magnolias, to later, compound ones such as sunflowers.Biology, pp. 1064.

To disguise the truth, you must spread confusion. Master Crook Mutation understands that well. If we want to discover the truth, we need to make some distinctions. When we make those distinctions, maybe we can also shed some light on the activities of Master Crook Mutation and his claims

At this point in time, the case stands as follows:

• There is evolution of proteins, for now the specific domain of Master Crook Mutation.
• There is evolution of species and/or populations, otherwise known as micro-evolution, the domain of Natural Variation and the Angel of Natural Selection; however, Master Crook Mutation claims he is THE authority there, since he is supposedly the source of new variation.
• There is macro-evolution, species changing into other types, the domain in which we will ask ourselves whether Master Crook Mutation is capable of realizing this.
  These levels of evolution relate to each other like a house, with a foundation and a roof. Molecular evolution is the foundation for the next levels. The house then supports the roof. Without molecular evolution, there is no evolution over the boundaries between species.

  		the roof: macro-evolution, originating new species or types
  		the house: evolution within species
  		the basis/foundation: evolution of genes

h. The Indictment: point mutations are an insufficient explanation for Macro-evolution
While sentences, machines, and other sorts of complex systems can undergo a certain degree of gradual functional change, there is invariably a limit beyond which the system cannot undergo further gradual change. To cross as it were from one "type" to another necessitates a relatively massive reorganization involving the redesign or respecification of all or most of the interacting component subsystems. Systems can undergo gradual microevolution through a succession of minor changes in their component structures but macroevolution invariably involves a sudden "saltational" change.
Michael Denton, Evolution: a theory in crisis.

Point mutations are, for an important part, responsible for what is sometimes called micro-evolution, or molecular evolution, that is to say: the continually progressing replacement of bases in homologous genes and of amino acids in the corresponding proteins during evolution. However, they probably were not involved much with the phenomenon which comprises much more of evolution, and led to the origin of increasingly complex life forms. Point mutations appear to have occurred with the same frequency throughout the entire evolutionary process and show no correlation to events that at certain moments have led rather abruptly to the emergence of new species.Christian de Duve, De levende cel (The living cell), part 2.

Point mutations or chromosomal rearrangements are themselves a limited source of variation for evolution because they can only alter a function or change on kind of function into another. ^[5]Genetic analysis, pp. 794.

Evidence is accumulating which suggests that protein sequence ^[6] evolution is not the only or even the most important basis of organismal evolution.
Biochemistry, pp. 131.

The occurrence of genetic monstrosities by mutation … is well substantiated, but they are such evident freaks that these monsters can be designated only as ‘hopeless’. They are so utterly unbalanced that they would not have the slightest chance of escaping elimination through stabilizing selection … the more drastically a mutation affects the phenotype, the more likely it is to reduce fitness. To believe that such a drastic mutation would produce a viable new type, capable of occupying a new adaptive zone, is equivalent to believing in miracles … The finding of a suitable mate for the ‘hopeless monster’ and the establishment of reproductive isolation from the normal members of the parental population seem to me insurmountable difficulties.
Ernst Mayr, Populations, species and evolution, pp. 235
(quoted from Access Research Network at www.arn.org)

Master Crook Mutation is subpoenaed! Serious doubts about him have been expressed. An indictment has been made. There are people who no longer trust him. His claims are cast into doubt. Furthermore, it is clear that he cannot cause macroevolution. He is too puny for that, since he cannot create new genes. He can only change existing genes. He cannot make 10,001 genes from 10,000. Still, no one really dares to kick him out of the House of Variation yet. On a larger scale, he may not have been the one who caused evolution, but on a small scale, he still does a lot of good in improving proteins. However that may be, we need to find a bigger brother, or cousin.

i.The Quest: evolution leaps forward
Once a new species appears in the fossil record, it tends to change hardly at all – even if it lasts millions of years. This pattern of non-change (we dubbed it “stasis”) flew in the teeth of what we had been led to expect – what evolutionists going back to Darwin had supposed we would really see if the fossil record were sufficiently complete: gradual evolutionary change through time. The motor of evolution – natural selection – was assumed to run all the time. ^[7] If environments remained stable, natural selection should act to perfect existing adaptations. Should the environment change, natural selection should gradually modify the features of organisms to keep them matched to their environmental needs. Either way, the evolutionary motor keeps running, and slow, steady transformation should be the rule.
…
In rediscovery stasis, Gould and I were holding evolutionary theory accountable to a nasty little fact of history: Most evolutionary change happens right off the bat, when a new species splits off from its ancestor and begins to go its separate evolutionary way. We called the pattern of change and stasis “punctuated equilibria”.
….
Whole ecosystems remain stable for millions of years.Not until ecosystems are perturbed and species start going extinct at high rates will evolution literally spring into action, producing new adaptations, new species – new players to rebuild the shocked ecosystems. In other words, with few exceptions, nothing much happens in evolution without extinction first disrupting ecosystems and driving many pre-existing, stable species extinct.
Niles Eldredge, What drives evolution, Earth magazine, dec. ‘96.

Eldredge and Gould could have make this their main message: Don’t worry Darwin, even if the fossil record were perfect you shouldn’t expect to see a finely graduated progression if you only dig in one place, for the simple reason that most of the evolutionary change took place somewhere else. … But no, instead they chose, especially in their later writings in which they were eagerly followed by journalists, to sell their ideas as being radically opposed to Darwin’s and opposed to the neo-Darwinian synthetics. ^[8]
…..
It isn’t true that Darwin believed that evolution proceeded at a constant rate. He certainly didn’t believe it in the ludicrously extreme that I satirized (in a parable that since it took the Israelites 40 years to get to Palestine, they were only doing 24 yards a day)…, and I don’t think he really believed it in any  important sense.^[9]
Richard Dawkins, The blind watchmaker.

According to the punctuated equilibrium theory, evolution proceeds by jumps – radical changes over short periods of time – separated by long periods of stability. ^[10] Gradualism refers to small-scale evolutionary changes in species, which ultimately might lead to reproductive isolation and speciation. Biology, pp. 1075.

Master Crook Mutation’s accomplice is no Big Brother. He needs to take great strides to fill in the gaps where Mr. Mutation is unable to. And these great strides are not the ‘rapid gradual sum of the point mutations’, because point mutations cannot explain increases in genes, or ‘gene growth’. The accomplice is probably related to Master Crook Mutation, so let’s just assume it is an Older Uncle.

j.The Older Uncles of Mr. Mutation? Then which mechanisms take care of macroevolution and/or gene growth?

1. No-one actually knows
Darwin's book was titled "The Origin of Species" despite the fact that he did not really address this question; over one hundred and fifty years later, how species originate is still largely a mystery. .^[11]
Chris Colby, The Talk. Origins Archive, Introduction to evolutionary biology.

Current explorations of novel genetic and developmental mechanisms, using the new techniques of molecular biology, may broaden the list of potential mechanisms for micro- and macroevolutionary change. Perhaps then we will know whether the sorts of microevolutionary speciation taking place as organisms at two ends of a cline become reproductively isolated can also lead to new genera, families, or even phyla.
Biology, pp. 1074.

In other words: we don’t know now, but we might find out later.

It is not known whether macroevolution proceeds by  “punctuations”. Nor it is clear whether unique mechanisms are required for either punctuations or macroevolution.
Biology, pp. 1075.

How does macroevolution arise? How do new species originate? How do new organs originate? How do the new genes that are supposed to do that originate? Through an Older Uncle? Who is he then? We don’t know!

2. Micro + time is macro
A few proponents of evolution solve the problem by pretending it doesn’t exist! They come up with the solution that macroevolution is the sum total of microevolution, that the Older Uncle is none other that Master Crook Mutation himself. Everyone is free to think as they like, but it seems to me that this is no longer in accordance with what is now known and even widely accepted (see the next point). The problem remains how the new, highly specialized and co-operative proteins (and therefore the genes that code for them) can originate, which are necessary for new organs, systems, functions, characteristics. How those new genes can cause a species to cross an existing boundary. How gene growth is possible.
The modern theory of the mechanism of evolution differs from Darwinism …
that it postulates that speciation is (usually) due to the gradual accumulation of small genetic changes. This is equivalent to saying that macroevolution is simply a lot of microevolution.(speciation is the origin of two or more species from one species, PMS)
Larry Moran, The Talk.Origins Archive, The modern synthesis of genetics and evolution.

Answer the following two questions:
1. Could the human eye have arisen directly from no eye at all, in a single step ?
2. Could the human eye have arisen directly from something slightly different from itself, something that we may call X ?
The answer to Question 1 is clearly a decisive no. The odds against a 'yes' answer for questions like Question 1 are many billions of times greater than the number of atoms in the universe. ... The answer to Question 2 is equally clearly yes, provided only that the difference between the modern eye and its immediate predecessor X is sufficiently small. ^[12] Richard Dawkins, The Blind Watchmaker

As we have seen, to invoke chance, on its own, as an explanation, is equivalent to vaulting from the bottom to the top of Mount Improbable’s steepest cliff in one bound. And what corresponds to inching up the kindly, grassy slopes on the other side of the mountain? It is the slow, one-step-at-a-time, non-random survival of random variants that Darwin called natural selection.Richard Dawkins, Climbing mount improbable, p.70.

What is this? Is this a new trick by Master Crook Mutation? Or is it the last twitch of his death throes? Why do some people continue to believe so stubbornly in his inviolability?

3.What it could be
In the past 30 years, geneticists have revealed a complex world of molecular inheritance, including genetic elements that can jump from one chromosome to another and, in some instances, even leap to unrelated organisms.^[13] If evolution is stability and change in genetic information, we now see molecular components to the evolutionary motor that bias the transmission of genetic information from one generation to the next.
Niles Eldredge, What drives evolution, Earth magazine, dec. ‘96.

Much more drastic intervention must have happened, and that probably consists of deletions, duplications, recombinations, transpositions, couplings, exchanges, viral invasions, and all other forms of genetic migration,^[14] the existence of which has been brought to light by modern research. In most cases, fooling around with orthodoxy like that must be immediately corrected, but in certain rare cases, perhaps in combination with a sudden climatological or other ecological change, the deviating product turned out to be better adapted than its ‘normal variant’. It became a phagocytic hunter in a sea with a shortage of nutrients, a fish that could live out of water or a tree-dweller exiled to the Savannah.
Christian de Duve, De levende cel (The living cell),  part 2.

Nature has devised many ways of changing the genetic architecture of organisms. We are now beginning to understand the molecular process behind some of these phenomena. Gene mutation, recombination between chromosomes, and transportation can all be reasonably explained at the DNA level. Far from merely producing genetic waste, these processes undoubtedly all have important roles in evolution. This idea is strengthened through the knowledge that the processes themselves are to a large extent under genetic control: there are genes that affect the efficiency of mutation, ^[15] recombination, and transposition.
Although mechanisms of transportation are sometimes used, the analogies between the transposable elements of phages, bacteria, and eukaryotes are striking. At present, it is not known if transposons are elements that normally play a role in the day-to-day transactions of the genome, as originally proposed by Barbara McClintock in the 1950s, or if they are pieces of “selfish DNA” that exist for no purpose other than their own survival. Whatever the truth of this matter is, transposons certainly represent a completely unexpected element of chaos in the genome, which geneticists have already harnessed into their team of analytical procedures. At the evolutionary level, transposons may be important in the sudden leaps that characterize the fossil record.
Genetic analysis, pp. 660.

To add new functions requires expansion in the total repertoire of genes through duplication and polyploidy (= multiplication of chromosomes, PMS), followed by a divergence between the duplicated genes, presumably by the usual process of mutation.
Genetic analysis, pp. 794.

Biologists have discovered ….. that genes may undergo duplication and divergence so that an extra copy of a gene arises by a mutational process. This duplicated copy is then free, in a sense, to evolve: while the original diploid (=double, PMS) set is still present to produce the phenotype and is still influenced by natural selection, the duplicated allele may have an altered base sequence and thus may yield new proteins with novel properties.
Biology, pp. 1027.

Mutation includes point mutation changes in DNA, as well as processes such as chromosomal rearrangement. Gene duplication and divergence, another category of mutation, can lead to families of related proteins.
Biology, pp. 1029.

Gene duplication is a particularly efficient  mode of evolution because one of the duplicated genes can evolve a new functionality through natural selection while its counterpart continues to direct the synthesis of the presumably essential ancestral protein.Biochemistry, pp. 131.

What we now see is that some sort of Older Uncle is indeed necessary who arranges an increase in genes in order to make new functions possible. Only his precise identity is not yet known. These suggestions have been made:

1.    Uncle of Duplication to Divergence (i.e. doubling and then change)’
2.    Uncle Transposon or Transposition;
3.    Uncle Virus, who sends his offspring to invade.

But there is also a fourth possibility.

Mutations in regulator-genes
Chance mutations in regulatory genes might also help to explain radical changes in structure that mark the beginning of major new groups of life forms. For instance, although most significant changes in a gene are likely to be detrimental to an organism (….), some tiny percentage may produce viable “hopeful monsters” – organisms that, although drastically altered, are still adapted to their surroundings and survive to reproduce.
Biology, pp. 1062.

Evidence (PeterS1) is accumulating which suggests that protein sequence evolution is not the only or even the most important basis of organismal evolution. There is, for example, more than a 99% sequence identity between the corresponding proteins of humans and our closest relative, the chimpanzee. ^[16] This is the level of homology observed among sibling species of fruit flies and mammals. Yet, the anatomical and behavioral differences between human and chimpanzee are so great that they have been classified in separate families. This suggests that the rapid divergence of human and chimpanzee stems from relatively few mutational changes in the segments of DNA that control gene expression, that is, how much of each protein will be made and when. Such mutations do not change protein sequences but can result in major organismal alterations.
Biochemistry, pp. 131.

Not only are there genes that code for proteins, there are also genes that control the development of the embryo. Such a regulator gene can turn whole groups of genes on and off, so that the right ‘parts’ are built at the right place and the right time. A small mutation in a gene like that can understandably have very serious consequences. This is therefore not an Older Uncle, but the (identical) twin brother of Master Crook Mutation himself. He just affects a different kind of gene, has a slightly different face. Could the people who say that macro is a whole lot of micro be right after all?

4.    Twin Brother Regulator Gene.(PeterS2)

5.2     The belief: there must have been evolution
More, I want to persuade the reader, not just that the Darwinian world-view happens to be true, but that it is the only known theory that  could, in principle, solve the mystery of our existence.Richard Dawkins, The blind watchmaker.

'There is no alternative,' says Dawkins.

I believe that this idea (of the hierarchical levels of evolution, PMS) will ultimately enable geneticists and paleontologists to agree on the form and content of that single evolutionary theory – a theory that must exist simply because life, with all its complexities and scales, from molecules to ecosystems, has had one single, integrated evolutionary history.
Niles Eldredge, What drives evolution, Earth magazine, dec. ‘96.

Taken as a whole, genetic changes consist almost without exception of gene alterations: mutations. The fact that they take place completely coincidentally is a fundamental characteristic of mutations.
Having come close to the end of our journey, such a claim can only sound unbelievable (italics mine, PMS). How often have we stood, speechless with admiration, in front of a piece of molecular apparatus that we could only describe in terms of ‘brilliantly designed’, or similar superlatives? And now we are asked to see all these wonders as nothing more than products of mere coincidence. It is simply ridiculous. And the evidence is still here before us, not only in the way we see genes at work, but also in the form of the historical document that this work has left behind in their structure and the structure of their products.
Christian de Duve, De levende cel (The living cell),  part 2.

The most important argument to indeed believe that evolution occurred is not the full comprehension of the mechanisms which caused it (on the contrary, they seem unbelievable, he says), but the fact, or ‘proof’, that life simply does exist. Evolution has to too.

One has only to contemplate the magnitude of this task to concede that the spontaneous generation of a living organism is impossible. Yet here we are—as a result, I believe, of spontaneous generation.
However improbable we regard this event, or any of the steps it involves, given enough time, it will almost certainly happen at least once. What we regard as impossible on the basis of human experience is meaningless here. Given so much time, the impossible becomes possible, the possible becomes probable, and the probable becomes virtually certain. One has only to wait; time itself performs miracles.
George Wald, "The Origin of Life," Scientific American , Vol. 190, August 1954, pp. 46.

…it is a considerable strain on one’s credulity to assume that finely balanced systems such as certain sense organs (the eye of vertebrates, or the bird’s feather) could be improved by random mutations. This is even truer of some ecological chain relationships (the famous Yucca moth case, and so forth). However, the objectors to random mutations have so far been unable to advance any alternative explanation that was supported by substantial evidence.
Ernst Mayr, Systematics and the origin of species, pp. 296.

Trust in Master Crook Mutation and his family is still unlimited and unashamed. There have been serious charges brought against him, but hope is not yet lost. There is a very simple reason for that: how would it work otherwise? We have no alternative. But, things aren’t all that bad, as we will see in part II...

But before we get that far, and now that we have been amply introduced to the actors, their characters, the place of operation, the stakes of the game, and the nature of the drama, we want to take a look at how the drama is unfolding.The following questions must be answered.

• Who is the rightful owner of the House of Variation?
• Can Master Crook Mutation improve genes and give them new functionality?
• Can Master Crook Mutation and the Angel of Natural Selection dethrone King Entropy?
• Who is Master Crook Mutation’s Older Uncle?
• Can this Uncle explain macroevolution?
• Can Master Crook Mutation cause macroevolution himself after all, through mutations in regulator genes?
• Does the entire Mutation family contribute collectively or each separately?
• In short, does gene growth happen and who causes it?