Thursday, March 19, 2015

The Theory Of Evolution: Modern Synthesis

Chapter 2.  The Modern Synthesis Goes To Work 

 [Note 1: the first chapter will be taken from the "Very Short Course On Evolution" already published, upper right column]

[Note 2: please feel free to offer criticisms, suggestions and error reports, thanks!]

To recap: Darwin’s theory, known as Darwinism, was developed by Charles Darwin’s observations of both fossil finds and exotic animals he observed during his time on the HMS Beagle. His theory, published in 1859 [1], was this: there is natural variation amongst animals and plants and that variation might be naturally selectable over very long time frames to produce plants and animals that are different from the originals.  Further, all plants and animals, in fact, all living things might have come from just one single ancestor. These theoretical premises became known as variation, natural selection, gradualism and common descent. Darwin also accepted Lamarckism, which posited that acquired characteristics or features might also be heritable.

“Darwin matters because evolution matters. Evolution matters because science matters. Science matters because it is the preeminent story of our age, an epic saga about who we are, where we came from, and where we are going.”
Michael Shermer [2]

The Process: A Short History of the Development of the Modern Synthesis

“The late Nobel laureate Sir Peter Medawar once remarked that “the reasons that have led professionals without exception to accept the hypothesis of evolution are in the main too subtle to be grasped by laymen.”
Sean B Carroll [3]

One might think – and hope – that a process which is declared to be science would have been developed using the standard tools of empiricism, namely induction of possible physical causation, induction of a theory of causation, deduction of physical effect from a physical cause, experimental design and implementation, analysis of experimental data for either falsification or support for the hypothesis, peer review, release of all data to the public for independent replication in order for the proposed knowledge to become objectively, if contingently, held. Otherwise, how could a concept be called objective knowledge produced by science, no matter how dearly it is held?

If science cannot or will not produce objective knowledge, then it must be subjectively held opinion and no matter how many hold this opinion, nor who they are, nor what their credentials, it still is just opinion and not objective knowledge.

“Progress depends on a blend of observation or experiment, which may suggest general principles, and of deductions from these principles that can ve tested aginast new observations or experiments. The search for knowledge of practical value can serve as a corrective to uncontrolled speculation…”
Steven Weinberg [4]

Fortunately there is a history which reveals how the Modern Synthesis came to be installed as “hardening of the synthesis” as Stephen Jay Gould put it [5], petrified it into scientific dogma, and which for many evolutionists became totally unchallengeable.

The Fight Over Neo-Darwinism

Neo-Darwinism was not easily won. The battle over Lamarckism was brutal. The turn of the century episode between Weismann and Spencer, who nearly came to blows over the issue of Lamarckism, is described by Stephen Jay Gould [6]:

“Passions ran high; I own Weismann’s annotated copies of Spencer’s articles, and his anger drips off the pages. The two warriors thrusted and parried on both high and low roads, mixing some good arguments about the structure of evolutionary explanation with ad hominem  charges of incompetence. Weismann disparaged Spencer for being merely a philosopher, and not a true scientist: ‘ I can only explain Mr. Spencer’s ignoring such cogent instances by supposing that, as a philosopher,  he is unacquainted with the facts by personal observation and that therefore they appear less weighty to him than to a naturalist; for I would not for a moment suppose that purposely evades the difficulties which face his opinion, as is the manner of popular orators and advocates – and alas! even of some scientists.’

Spencer, in his touche’, replied, not entirely without justice as we shall see, that Weismann had hidden poor arguments under the cloak of authority as a practicing scientist: ‘Now it is doubtless true that as a naturalist he may claim for his ‘opinion’ a relatively great weight. Still, in pursuance of the method of science, it seems to me that something more than an opinion is required for a far-reaching theory.” [Emphasis Added]

Weismann became the man known for “disproving Lamarckism”, according to Gould.  Further, says Gould,
“Weismann’s strong anti-Lamarckian argument does not rest upon an experiment, or an empirical observation at all. The rejection of soft inheritance arise as a logical deduction from Weismann’s most distinctive contribution – his theory of inheritance and the continuity of germ plasm…

Weismann wrote in his ALLMACHT paper (1893, p 608): ‘Nature has carefully enclosed the germ-plasm of a germ-cells in a capsule, and it is only yielded up for the formation of daughter-cells, under most complicated precautionary conditions’

Once Lamarckian inheritance becomes impossible, Weismann’s argument for the Allmacht of selection proceeds in four logical steps. This fourfold development will strike most modern scientists as curious and unsatisfactory, for the sequence not only requires no empirical contribution, but actively denies the possibility of effective input from this conventional source of scientific affirmation. The argument breaks no rules of logic, but several of its premises are (to say the least) not self-evidently true.” [Emphasis Added]

In other words, “I am a scientist; no actual disciplined science is needed; trust me.”  Darwin’s story-telling-as-science took full hold and became the defining process of science for evolutionary theory.

By the turn of the century, Neo-Darwinism was accepted, which allowed for all of Darwin’s original premises, but disallowed Lamarckism.

Trouble For The Principle of “Variation”: The Hardening Around Mutation

In the 1930’s and ‘40’s there was a considerable turmoil amongst evolutionary theorists. This resulted in the development of another required premise for evolution: mutation. Mutation was required in order for the radical changes to occur which were observed in the fossil record; mere variation was not enough.  And Mendel’s genetics, which threatened Darwinism, were force fit into the new evolutionary theoretical “synthesis”.  Mutation, Selection, Deep Time, Common Descent, with some Mendelian Genetics of a sort. This was known as the Modern Synthesis, and became the dogma for evolution.

When it comes to the development of the Modern Synthesis, disputes similar to the Lamarckian crisis arose. However, Gould documents a “hardening” of the concepts, and the hardening has been verified by other historians. Gould describes the realization of a trait which started with Simpson, who had modified his original position, but hid that fact: “Simpson had minimized the appearance of change by retaining the same terms while profoundly altering their meanings”.  He had become adaptationist without admitting his changeover.

Gould found that Dobzhansky, Mayr, and “other key figures”,
 “…all had moved from pluralism to strict adaptationism – and along a remarkably similar path [to that of Simpson]. I began to view this transition as the major ontogenetic event of the Synthesis during its second phase. I christened this change as the hardening of the Synthesis…”. [7]

But the Modern Synthesis had hardened without critical examination in some areas. For example,
Dobzhansky’s willingness to accept an incomprehensible literature, and the later acquiescence of so many leaders from other subdisciplines (largely via Dobzshansky’s “translation”), testify to a powerful shared culture among evolutionists – a set of assumptions accepted without fundamental questioning or perceived need to grasp the underlying mechanics. Such a sense of community can lead to exhilarating, active science (but largely in the accumulative mode, as examples cascade to illustrate accepted principles).  As a downside, however, remaining difficulties, puzzles, anomalies, unresolved corners, and bits of illogic may retreat to the sidelines – rarely disputed and largely forgotten (or by the next generation, never learned).  This situation may sow seeds of an orthodoxy  that can then become sufficiently set and unchallenged to verge on dogma – as happened in many circles, at least among large numbers of epigones, at the acme of the Synthesis in the late 1950’s and 1960’s.”[8]
[Emphasis Added]

So were these celebrity scientists doing actual science?  Let’s take a quick look at the definition of science, from the National Academy of Sciences:

Definition of Science
The use of evidence to construct testable explanations and predictions of natural phenomena, as well as the knowledge generated through this process.” [9]

Clearly the Modern Synthesis came into being without any physical evidence other than the fossil record of animals existing in prehistory and being found in layers.  Evolution was not found; it was created without benefit of direct evidence for it, without a thought of testability in any explanations, and without any capability of predicting any outcome, whatsoever, except for finding certain remains in certain geological layers.  It was a series of meta-hypotheses which had hardened purely by mutual acceptance within a select and credentialed circle.

The Modern Synthesis Becomes Dogma

By the 1950s the Modern Synthesis had solidified into the standard apologetic for evolution, and the evolutionary community was ready for the advent of DNA as explanatory for genetics and genomes in general.  DNA provided a theoretical matrix to support the new but vague concept of mutation as the necessary change in a genome which could be selected naturally. Thus a new genome could be produced with new features, perhaps new organs, and speciation which deviated from that genome’s prior species, just by mutating the structure of DNA.

There was little left to question about evolution, it seemed.  So the focus changed from finding new causes to more in-depth analysis of those causes of mutation, the frequency and extent of mutation, the possibility of beneficial mutation, and natural selection of those beneficial mutations. These issues would necessarily have to be justified, if the combination of mutation/selection were to be declared causal for evolution as found in the fossil record.

There were challenges to the dogma.

“Perhaps our Darwinian prejudice for regarding selection as by far the most effective, or virtually the only important, process of evolutionary change arises more from the parochialism of our organismal focus (given our own personal residence in this category) than from any universal characterization of all levels in evolution.”
Stephen Jay Gould [10]
And there were some obviously desperate explanatory supporting hypotheses, which were necessary due to the failure of the fossil record to support the Modern Synthesis. Gould proposed the theory of Punctuated Equilibrium [11], which stated that evolution might remain stable, without change (stasis) for long periods but might be punctuated with periods of brief but rapid genomic change (rapid evolution).  This was necessary in order to counter the theory that deep time (gradualism) was an absolute requirement for evolutionary change but which was not a consistent feature of the fossil record.

But this new theory held that no evidence actually was evidence for quick evolution (e.g. in the Cambrian explosion).  This was hardly a causal theory, and not much different from what Gould himself deprecatingly called “Just So Story Telling” as the scientific methodology of evolutionary “science”.  In fact, storytelling was all that Darwin had to offer for his theory.  That he thought it plausible enough to be actual science is one thing. That many others declared its plausibility to be actual science and even truth is another.

But the theorists took to heart the issues which needed more careful explanation, even though the mechanics of evolution itself were still undefined except at the meta-theory level.


“It is now clear that gene mutations and structural and numerical chromosome changes are the principle sources of variation”
Gould, [12]

Mutational causes were known to produce cancers and defects in progeny, defects which were generally selected out of the genome.  The deleterious mutation rate was placed at a level of 0.12 to 0.30 mutations per person per generation [13].  More recently the rate is placed at 100 to 175 nucleotides per person per generation [14].  And the human mitochondrial mutation rate is placed at nearly “one mitochondrial mutation per person per generation within the reproductive cell line” [15].

But there are other types of mutations as well, the most serious of which is “macro-mutation”, which affects entire DNA sequences, much as changing a single word throughout an instruction manual changes the meaning within the manual.  Such changes are not logically for the better, producing by accident a better product than originally produced by following the original manual without random changes.

As an example of deleterious mutation occurrence, there is this: for a lower threshold, given 6 billion humans and 100 (very conservatively) new mutations per human, there have been 600 billion new mutations in one generation.  That comes to 200 mutations for every nucleotide in the human genome, in just one generation. If this sounds serious, it is.  Because of the following, all of those mutations are to be considered deleterious:

From Sanford:
“In June of 2007 a large international consortium of genome scientists (under the name ENCODE) published their finds in a set of 29 scientific papers. These findings have stunned the genetics community (Kaperanov et al., 2007).  They show that the human genome is vastly more complex than they had expected, and that essentially all of the genome is transcribed – most of it in both directions. They conclude that most nucleotides are not only functional but are poly-functional, having multiple roles. This means that the genome’s functionality exceeds 199% (most of both strands of DNA are functional). In this light, no mutations should be considered “perfectly neutral”, and essentially all mutations must be considered deleterious. This means that the real deleterious mutation rate in man is nothing less that staggering – well over 100 mutations per person per generation! This is more than an order magnitude greater than was considered possible just five years ago.” [16]

The impact is this:
(a) there are no neutral mutations which can be carried forward to combine with other neutral mutations at some later time in order to ultimately produce beneficial outcomes;
(b)  genomic entropy is, in fact, not just dominant, it is the only mutation characteristic which applies,
(c) There exists an “error catastrophe” in the form of human-wide degradation leading to extinction.  Bernardes [17] called it “mutational meltdown”.

Another factor to consider is that the DNA code is somewhat redundant: according to Yockey, eukaryotic genomes (multicellular) have 8 to 20% duplicates [18]. These serve as error corrections, along with other internal error correction devices [19], thus limiting not only deleterious mutations but also beneficial mutations as well.


Given that virtually all mutations are deleterious, Kumura [20] created a visual conception of the truncated distribution, and added his “no selection zone”, which encompassed most of the mutations in the distribution.

Fig. 1. The Kimura Distribution, showing the “No Select Zone” for mutations.

And the Kimura Distribution of selectable mutations shows that while only a few negative mutations are selectable, no positive mutations (zero) are selectable. [21]

Fig 2. Kimura Distribution with addition of positive mutations.

If one assumes that some number of positive mutations do occur, then their placement in the distribution is shown in Fig. 2.  They fall well within the No Selection Zone.  This along with the findings of the ENCODE genome scientists, demonstrates the impossibility of selection of positive traits due to mutation. [22] (Both graphs are from Sanford’s “Genetic Entropy”, p31, 32.)

From an external view, Pigliucci and Muller make this statement [23]:

“Hence the organisms themselves represent the determinants of selectable variation and innovation. At the theoretical level, this shifts a significant portion of the explanatory weight from the external conditions of selection to the internal generative properties of evolving phenotypes”.

In other words, mutations (external causation) are no longer thought to be significantly causal; so they are now replaced by internal causes occurring naturally (perhaps epi-genetically).  The removal of mutations as causal means that selection is not a necessary feature of evolutionary theory.

Selection has never been much help: mutations at the nucleotide level are not selectable.  There are at least six levels of removal of nucleotides from the whole organism. It is at the whole organism level that natural selection would work. Yet, even given the error correction capabilities and protein competition for activation, some errors still make it to the whole organism level.  Virtually all of those will not be benign or beneficial.  And any selection that is done will be done to purge those whole organisms which exhibit negative mutations that affect the whole organism.

Genetic Causality:
Pigliucci and Muller again [24]:

“But gene centrism necessarily disappears in an extended account that provides for multi-causal evolutionary factors acting on organismal systems’ properties, including the non-programmed components of environment, development, and inheritance.”

The focus thus becomes, “genes as followers”, while “evolution progresses through the capture of emergent interactions into genetic-epigenetic circuits which are passed to and elaborated on in subsequent generations.”

Translation: there are new relationships between genes which are switched on or off internally, and for whatever reason.  The new relationships become something new, which is passed along.  It is thus kept as a new genetic feature, and doesn’t even require selection in order to be perpetuated.  Evidence for this will be discussed in coming chapters.

As for the Darwinian theory of gradualism (aka, “deep time”, originally thought to be required for serious changes to be gradually selected into new, evolved creatures), the deep time theory was killed by the fossil record itself.  The development of all the major phyla in the short time (5 to 15 mya) of the Cambrian Explosion negated the need for deep time.

And as an aside, the Cambrian Explosion has wounded the concept of common descent (common ancestry) as well, because even after 250 years of fossil excavation there has been no common ancestor found for all the phyla which are found in the Cambrian Explosion.

In a final blow to natural selection, mutation, gradualism and gene-centrism, Pigliucci and Muller say this:

“The overcoming of gradualism, externalism, and gene centrism are general hallmarks of the Extended Synthesis, whether in the forms presented here, or in various other accounts to a similar effect published since the late 1990s.” [25]

With this, it appears that (for some evolutionary theorists at least) Darwinism is dead.

Failing both all the original premises, and all the criteria for being called a “science” has not deterred either evolutionary “scientists” or evolutionary fans from claiming its high status, even as the unifying theory of biology, and further to declare skeptics to be anti-science.

Unification Theory

The unification of all empirical theories into one coherent science has been addressed by Carnap; Neurath, and explained by Brand Blanchard

“And if two statements are so related that they are always true together, and always false together, they are ‘equipollent’; each is the logical equivalent of the other and may at will be translated into it. If such equipollence is recognized, the road to the unity of science is clear.  Every factual statement of in every science will have an identical test of meaning and truth. All laws will be interconnected as parts of a single system. As Carnap put it, science will become intersensible, intersubjective, and universal. It will be intersensible because we need no longer regard tasted sound and colour as incommensurable data; they can now all be read as physical changes differing only in physical ways. Again science will be subjective because, when we say for example, ‘the room is hot’, we shall not mean that we have a private feeling inaccessible to everyone else, but that the room has  physically a certain temperature, which can be tested by a thermometer open to the observation of all.  And the language of science will be universal because ‘every sentence of any branch of scientific language is equipollent to some sentence of the physical language without changing its content. Thus the new criterion of meaning, interpreted as requiring ‘physicalism’, becomes the most powerful of engines for the unification of science.” [26]

What would it take for the evolutionary hypothesis to become a unifying theory, even if merely unifying all of biology, and even if merely under the authority of empirical science?  Evolutionists frequently cite Maxwell’s unifying theory of electricity and magnetism. How does Modern Synthesis evolution compare?

1. Comprehensive application to all subsets:
Modern biological science does not depend upon evolutionary principles.  Evolution thus serves no need in biological study or progress.

2. Testability:
First, historical events are not empirically, experimentally testable.  Second, laboratory induced genomic changes would be intelligently designed, forcing changes, not natural changes.

3. Falsifiability:
Some have claimed that finding a pre-Cambrian rabbit would falsify evolution. But evolution is so malleable, having no elastic limits to its meta-hypotheses, that new hypotheses would jump up to cover that event – or any other fossil induced “refutation” of the dogma.  That has already happened, an example being the constant re-definition of “fossilization”, which now covers soft material which is not mineralized. [27]  Rather than adapt hypothesis to observation, observations are redefined to be congruent with hypothesis.

4. Accurate predictability:
Evolutionary hypothesis predicts no biological outcomes.[28] It can predict where fossils might be found, which is not a validation of evolution. But it also predicts fossils which have not been found (common ancestor for Cambrian Explosion), and it predicts fossils which cannot be found (first life).

5. Capable of replication:
By virtue of the “deep time” issue in the Modern Synthesis, none of the fossil record could be replicated as the events supposedly actually occurred (which is not knowable).  Creation of life or creatures in the lab would be an “intelligently designed” event, and therefore not a model of actual historical events.

Note that Maxwell’s unification does pass these requirements of a unification theory. Evolution, under the Modern Synthesis, does not.  In fact, it cannot even legitimately pretend to do so, because it has no causal theories, being mostly hyperbolic meta-hypothetical speculations.

And so we return to the issue of “what is science, actually, and what is not?” In Chapter One, science was defined as the generation of objective knowledge about the physical universe under the principles of empiricism.

Let’s look at the National Academy of Sciences answer to the question, “Is Evolution a Theory or Fact?”
“It is both…

Many scientific theories are so well established that no new evidence is likely to alter them substantially. For example, no new evidence will demonstrate that the Earth does not orbit around the sun… or that living things are made of cells… (etc.)… Like these other foundational theories, the theory of evolution is supported by so many observations and confirming experiments that scientists are confident that the basic components of the theory will not be overturned by new evidence.” [29]

How many failures can we find in that assertion?
(1) Orbiting planets and cell theory have nothing to do with the validity of Evolutionary Theory. The entire first paragraph is laden with Appeal to Authority logic failure.

(2) Evolution is given stolen authority and credence by virtue of its false inclusion with “other foundational theories”.

(3) There are no observations of macro-evolution. None.

(4) There are no confirming experiments of macro-evolution. None.

(5) If there is “new evidence” it would actually be the first actual empirical evidence in support of Evolution, which currently has none.

(6) The need for “testability” as indicated on the prior, facing page, has been falsely claimed to exist.

(7) The Modern Synthesis is currently being overturned in all its aspects, precisely because there is no evidence to support it, and all of its premises have been found to be untenable (false).

So what about the claims of all that evidence which exists supporting evolution?  Well, disregarding fossil finds and speculations about them, and also disregarding the obligatory referencing of not-negating-evolution-more-study-money-needed in every biology paper printed, actual empirical evidentiary claims are sparse.  There are several famous examples.

Modern Synthesis Evidentiary Examples

1. The Grants and the Famous Darwin Finches

One of the most interesting Darwinian Evolutionary research projects has been that of the Grants. Drs. B. Rosemary Grant and Peter R. Grant are the spousal team who spent over a decade starting in 1973 studying Darwin’s Finches on the Galapagos Islands. These studies have been raised to mythical levels in the writings of evolution for public consumption.  Here is an example from Jonathan Weiner:

“The Grants are leaders of this field, and they are among its ideal representatives. Year after year they go back to the celebrated place in the study of evolution, the place that helped lead the young Darwin to his theory: the Galapagos, the Enchanted Islands.  There they observe Darwin’s finches, the birds that Darwin was the first naturalist to collect; the birds whose beaks inspired his first veiled hints about his evolutionary theory; the birds whose portraits in textbooks have now introduced so many generations to Darwinism that they have become international symbols of the process, totems of evolution, like the overshot brows and cumulous beard of Darwin himself. Now the Grants’ work on Darwin’s finches is entering the textbooks, too. This is one of the most intensive and valuable animal studies ever conducted in the wild; zoologists and evolutionists already regard it as a classic. It is the best and most detailed demonstration to date of the power of Darwin’s process.” [30]

But what, exactly, did the Grants actually find in all their years of observation of Darwin’s famous finches? What, exactly, justifies the hyperbolic elevation of the Grants to superstars of evolution? Here are the final results of the Grants 13 year study, in their own words:

“However, the change in mean beak length that occurred as a result of selection in the early phase of the drought was counteracted later in the drought in the opposite direction on bill depth, which is positively correlated with bill length. The overall result was no net change between the end of breeding in 1983 and the resumption of breeding in 1986.

The main generating processes are mutation, which we cannot study, and introgression of genes.
Including probable hybrids in the sample of breeding birds had the effect of increasing the coefficient of variation by 20 percent, and increasing the variance by 35 percent. Hybrids reproduced successfully, but did not live long and contributed less than nonhybrids to total breeding.

Thus variation is maintained by the opposing processes of introgression and selection. They were not in a state of balanceduring the decade. By the end of the study a significant reduction in the phenotypic variance of beak depth  and beak width had taken place among females, andnonsignificant differences in the same direction were apparent among the males. Given the high heritability of , it I possible that a reduction in genetic variation had occurred as well, as a result of selection.” [31]

So they found no permanent change and virtually no effect from hybridization due to early death of hybrids.  They speculate that the oscillation around stasis was produced by selection.  Further, when they thought they spotted “Population subdivision” due to a difference in finch songs, they were later forced to conclude:

“These initial signs of population subdivision subsequently disappeared.”

And this:

“Females, however, do not pair preferentially with males singing a particular song type; paternal song type does not influence their choice of mate, and so there is no reproductive subdivision of the population along the lines of song through assortative mating. Instead, females choose mates on the basis of plumage and courtship behavior.”

The Grants wrote an entire book, “The Evolutionary Dynamics of a Natural Population” [31], to say that they found nothing which even suggested speciation changes in the population of Darwin’s Finches they monitored, nor did introgression and hybridization take hold. What they did find was beak length changing in response to food availability, a micro-evolution variation which oscillated within boundaries.

2. The Lake Malawi Cichlids

There are said to be some 500 species of cichlids (fish) in Lake Malawi, Africa. Of these, some 300 are said to be “mbuna”, or rock dwellers. The study [32] produced a dendogram (tree graph) showing their take on the relationships between different, isolated groups of cichlids, based on coloration. Included in the populations is the originating population, which still lives in the lake.

However, they also observed interbreeding, and they found that the variability of the genomes within each pocket population was far broader than the differential between genomes. Further, the DNA indicated a high degree (over 50%) of polymorphism, meaning that within a population many forms of DNA variability exist at a single DNA location.

Is there any reason from this to think that new characteristics have “evolved”? Given that the main morphological change is the mouth configuration, and that this characteristic variability is common within color-designated speciation, and given the ability to crossbreed, there is no morphological reason.

Given that the DNA variability under discussion is subtractive, not additive, there is no reason to think that the variations are not just subsets or subspecies of the main, overall species, which still exists.

Since the time frame assignments are based on differences in the number of common DNA markers seen, and there is no actual clocking mechanism involved other than this inference, there is no reason to think that this is meaningful, especially since the markers are not defined as to purpose, and might be meaningless to the presumed speciation.

To summarize: given the stated ability to cross-breed, plus the existence of members of the original population, and the lack of any reason to think that there was speciation based on new features, the conclusion follows that this is consistent with variation within a genome: subspeciation; not with evolution beyond the original genome.

Within this study there is no reason given to believe that the differences in coloration are an added feature, or that the differences are anything other than subtractive. In fact, their conclusion is merely that there are few “bottlenecks” to the creation of these populations. That would be expected in subpopulations of a single species, and is not in any sense macroevolution.

3. Evolution Of A Key Innovation In E-Coli

This experiment [33], which was begun in 1988 and is still progressing, was designed to watch for long term evolutionary activity in colonies of e-coli that were begun from identical clones:

“The founding strain is strictly asexual, and thus populations have evolved by natural selection and genetic drift acting on variation generated solely by spontaneous mutations that occurred during the experiment. Thus, the LTEE allows us to examine the effects of contingency that are inherent to the core evolutionary processes of mutation, selection, and drift.”

The environmental inducement to adapt is the use of a citrate in the plate, along with a very limited amount of the normal nutrient. E-coli are known to be able to use citrate as a nutrient once it is inside the cell, but lack a functional transport mechanism to bring it in from the outside. So in an environment high in citrate but low in normal nutrient, will the e-coli evolve a mechanism to transport the more available nutrient?

After more than 33,000 generations and “billions of mutations”, strains of Cit+ e-coli were found, and the colonies became dominant, although sharing the plates with original Cit- e-coli colonies.

The experiment was designed with built-in replicability by having frozen samples of the cultures at every 500 generations. This allowed the experimenters to “rerun” the experiment through the development of the Cit+ strain, to see if it would repeat. If it did repeat, it would mean that a prior, “historical” event must have been present. The Cit+ strain did, in fact, appear in the repeated experiments. This means that even with a different mutation experience, the Cit+ strain appearance was inevitable in these colonies.

And in fact, that is what was found.

“What physiological mechanism has evolved that allows aerobic growth on citrate? E. coli should be able to use citrate as an energy source after it enters the cell, but it lacks a citrate transporter that functions in an oxygen-rich environment. One possibility is that the Cit+ lineage activated a ‘‘cryptic’’ transporter (41), that is, some once-functional gene that has been silenced by mutation accumulation. This explanation seems unlikely to us because the Cit+ phenotype is characteristic of the entire species, one that is very diverse and therefore very old. We would expect a cryptic gene to be degraded beyond recovery after millions of years of disuse. A more likely possibility, in our view, is that an existing transporter has been coopted for citrate transport under oxic conditions. This transporter may previously have transported citrate under anoxic conditions (43) or, alternatively, it may have transported another substrate in the presence of oxygen. The evolved changes might involve gene regulation, protein structure, or both (61).

“In any case, our study shows that historical contingency can have a profound and lasting impact under the simplest, and thus most stringent, conditions in which initially identical populations evolve in identical environments. Even from so simple a beginning, small happenstances of history may lead populations along different evolutionary paths. A potentiated cell took the one less traveled by, and that has made all the difference.”

The results are therefore indeterminate in the sense of knowing whether a new feature has been developed, or a long dormant one has been re-enabled, epigenetically. Until this is resolved, the appellation “evolution” – in the long-term, new feature, new creature sense – is not appropriate. The use of “evolution” to cover any change whatsoever is the sense in which it seems to be used here. I don't agree that it is less parsimonious to assume that a dormant gene is being revived; I think that testing should be done first, and conclusions drawn later.

This is a well designed experiment that deserves watching as new sub-experiments are designed and implemented, and as more definitive DNA analysis resolves the issue of what the Cit+ mechanism actually consists.

4. The Wall Lizards of Pod Mrcaru

These lizards are not indigenous to the island of Pod Mrcaru and were introduced 36 years ago. In 2008, a paper was released regarding a study of the lizard [34], and its changes from the "ancestral population". Most of the changes were morphological, involving the shape of head and jaw, with some changes in social habits too. But the most striking claim is that the lizards had developed a new feature: a cecal valve in their digestive tract, which did not exist in the ancestral population. The cecal valve has utility because it allows the slowing of digestion, which is needed to accommodate the increase in the vegetative proportion of the diet (similar to valves in ruminant digestive tracts which differentiate “stomachs”).

 According to the paper,

"The relatively large fraction of leaves included into the diet of
lizards in the introduced population of Pod Mrcaru has apparently
also resulted in the evolution of cecal valves, a structure
previously unreported for this species and rare in this family and
scleroglossan lizards in general".

Since this occurred in roughly 30 generations, it is being referred to as rapid evolution. And being an apparently new organic type feature, many internet evolution apologists seem to accept this as having evolved and being absolute proof of "observed evolution". However, this blatantly ignores other possibilities, chief among which is that the gene for the cecal valve pre-existed and was turned off by negative mutation during disuse of the feature.

This could be supported or falsified by finding the differences in DNA between the Pod Mrcaru population and its ancestral population, and thus determining if the gene is novel, or if it is previously there, but turned off.

I contacted an author of the paper, Dr. Duncan J. Irschick, to ask if the DNA testing had been done to determine the genetic source of the cecal valve. Dr. Irschick replied, "not yet!"

That seems to put closure on the current claim: it is not known if the "new feature" is actually new, or if it pre-existed in an OFF state, even 6 years later. The fact that a tiny percentage of close relatives do have the feature suggests that the feature might have been necessary prehistorically, but was shut off as the lizard's environment shifted toward high populations of insects, relieving the need for plant matter. Parsimony suggests that the valve did not evolve from nothing in 30 generations, especially given a more likely source.

I also received this message from Dr. Anthony Herrel [35].

We're still working on getting a handle on those questions. We are
currently analyzing the microbial communities in the lizards from the
two islands. A next step will be to raise lizards from the two islands
in a common environment to test whether the presence of the cecal
valves is genetic or not. Once we have understood these elements we
can then ask the question pertaining to the underlying molecular

Sorry for not being able to address your question yet, but we're
working on it.


The response from these authors has been rapid, kind and polite. While I'm not sure why the molecular analysis must wait on the outcome of these tests; it will be interesting to see what they produce.

The possibility remains that the genetics already were available, and that were switched in when needed.

Conclusions regarding the evidence for evolution: No reported evidence of which I am aware shows mutation and selection as causal for changes in a biological population. When “evolution” is reported, it has always been either misreported or micro-evolution (remaining within the original genome) and neither speciation nor a significant new biological feature which was previously not in the genome.

Holes in the Meta-Hypotheses

But there is still more to be considered here. The Modern Synthesis addressed evolution at a meta-hypothetical level which is far removed from physical causality. It is said to represent a unifying theory for biology, and is the defining story of the saga of life in our universe despite being able to give no specific causation and no prediction for biological outcomes. And it does not even attempt to address some very important issues regarding life and living things.  Here is a partial list of issues which evolutionary theory as rigidified in the Modern Synthesis has not and cannot address:

1. None of the characteristics of being human at the whole organism level: agency; intellect; qualia; empathy; grief; intentionality; comprehension.

2. Abiogenesis (first life).  And the logical failure of the Central Dogma.

3. Common Descent for the Cambrian explosion.

4. Information content: non-compressible, semantic, possessing utility for both creation and activation.

5. Complexity of original cell.

6. Communication Groups, codes, channels.

7. Protein factories; necessary in prokaryotes.

8. Eukaryotic integration of multi-cellular coherence.

9. Complete lack of empirical rigor; testability, falsifiability.

10. Radical adherence to a belief system without support from objective knowledge.

These issues will be discussed in subsequent chapters with regard to the Extended Synthesis and the new meta-hypotheses which replace the Modern Synthesis.

The advent of the Extended Synthesis marks the death of the Modern Synthesis and all its confident claims, and demarks a new era of differing claims, made with similar confidence. These new claims will be addressed in upcoming chapters.

“My skepticism is not based on religious belief, or on a belief in any definite alternative. It is just a belief that the available scientific evidence, in spite of the consensus of scientific opinion, does not in this matter rationally require us to subordinate the incredulity of common sense. That is especially true with the regard to the origin of life.”
Thomas Nagel [36]

“Even a summary investigation of the history of discontents with the [Modern] Synthesis suggests that it is first and foremost a loosely and flexibly structured network of concepts and models rather than a ‘theory’ according to old-style hypothetico-deductivism.”
Werner Callebaut [37] [emphasis in original].

“There is no need to placate the ghost of neo-Darwinism; it will not haunt evolutionary theory much longer”
D. J. Futayama, [38]

“If, as seems obvious to me, the [Modern] Synthesis has no essence, its extensions are negotiable.”
Werner Callebaut [39]

Despite this, the public is constantly hounded with charges of anti-science if they harbor any doubts about evolution:

“Evolution is the fundamental idea in all of life science, in all of biology.

[Doubt is] equivalent of trying to do geology without believing in tectonic plates.

You're just not gonna get the right answer; your whole world will be a mystery instead of an exciting place.

Your world becomes fantastically complicated when you don’t believe in evolution. Here are these ancient dinosaur bones, these fossils; here is radio activity; here are distant stars which are just like our star but are at a distant point in their life cycle. The idea of Deep Time, of billions of years, explains so much of the world around us. If you try to ignore that, your worldview just becomes crazy, it’s just untenable, it’s self-inconsistent.

And I say to the grownups, if you wanna deny evolution and live in your world that’s completely inconsistent with everything we observe in the universe, that’s fine. But don’t make your kids do it, because we need them, we need scientifically literate voters and taxpayers for the future. We need people that can… we need engineers! We need people that can build stuff and solve problems.
Bill Nye, The Science Guy [40]

Fossils and deep time are essential causal factors and their acceptance is necessary for “scientifically literate voters and taxpayers for the future”? Why? And how, exactly, do engineers depend on fossils and deep time to perform their intellectual tasks? Well, they do not. Nye is a TV regular, and yet is one of the most egregiously ignorant of the radical public apologists for evolution. There must be an underlying reason, an emotionally driven cause for those like Nye whose vision of the future is that society cannot survive without evolution as doctrinally ubiquitous. Like Nye, they appear to live in actual palpable fear of the denial of evolution as fact.

This aspect of evolution is a psychological and socio-political issue, not a scientific hypothesis. It will be considered in an upcoming chapter.

1. Charles Darwin; “On The Origin Of The Species”, 1859

2. Michael Shermer, quoted by Jerry Coyne; “Why Evolution is True”; Viking, 2009, p xv.

3. Sean B. Carroll; “The Making of the Fittest”; Norton;2006; p 35.

4. Steven Weinberg, theoretical physicis;, “To Explain the World: The Discovery of Modern Science”; HarperCollins, 2015;  p202.

5. Stephen Jay Gould, “The Structure of Evoutionary Theory”; Belknap/Harvard Univ. Press; 2002; p 520, 521.

6. Ibid., p198.

7.Ibid., p 522.

8. Ibid. p 320.

9. National Academy of Sciences; Institute of Medicine; “Science, Evolution, and Creationism”, 2008; p10.

10. Stephen Jay Gould, “The Structure of Evolutionary Theory”, p 75.

11. Ibid. p 994 – 999.

12.Ibid., p 525.

13. J. C. Sanford; “Genetic Entropy”; FMS Pubs.; 2005;  p33; (Morton, Crow and Muller, 1956)

14. Ibid. p34; (kondrashov, 2002; Nachman and Crowell, 2000) A nucleotide is one bit of information in DNA and RNA, which is contained in the 4 bit quadruplet of DNA and RNA.  DNA and RNA have 64 letters in their alphabet.

15.Ibid. p35.

16. p 41.

17. A. T.  Bernardes, 1996 ; Physica ACTA 230:156-173.

18. Hubert B. Yockey; “Information theory, Evvoution, and the Origin of Life”; Cambridge, 2005; p38
19. Cooper-Hausman, p200-201; 213.

20. M. Kimura, 1979; PNAS 76:3440-3444.

21. J. C. Sanford; Genetic Entropy; p 32.

22. Both graphs are from Sanford’s “Genetic Entropy”, p31, 32.

23. Pigliucci and Muller, Eds.; “Evolution; the Extended Synthesis”; MIT Press, 2010; p13, 14.

24. Ibid.; p14. (top)

25. Ibid.; p14. (bottom)

26. Brand Blanchard; “Reason and Analysis”; Paul Carus Lectures, Series 12, 1962; Open court Pubs; p213, 214.

27. Science Against Evolution; ; 1999.

28. Jerry Coyne; “Why Evolution Is True”; Penguin, 2009; p222.

29. National Academy of Sciences; Institute of Medicine; “Science, Evolution, and Creationism”, 2008; p11.

30. Jonathan Weiner, “The Beak of the Finch”, Vintage, 1994, pg 9.

31. R. B. Grant and P. R. Grant; “The Evolutionary Dynamics of a Natural Population”, 1989; Univ of Chicago Press; pp282-285.

32. Proc. Natl. Acad. Sci. USA Vol. 96, pp. 5107–5110, April 1999.

34. “Rapid large-scale evolutionary divergence in morphology and performance associated with exploitation of a different dietary resource”  PNAS, 105 12, 3-25-08, p4792.

35. personal communication.

36. Thomas Nagel, “Mind and Cosmos: Why The Materialist neo-Darwinian Conception of Nature Is Almost Certainly False”, Oxford Univ. Press, 2012; p7.

37. Werner Callebaut;  Extended Synthesis, p 457.

38. D. J. Futayama, DJ, “Sturm und Drang”; Evolution 42; p222. Per Callebaut, TES, p456.

39. Werner Callebaut; Extended Synthesis, p458.


  1. "This was necessary in order to counter the theory that deep time (gradualism) was an absolute requirement for evolutionary change but which was not a consistent feature of the fossil record."

    Gradualism over vast amounts of time was a key part of Darwin's theory:
    "On the other hand, I do believe that natural selection will always act very slowly, often only at long intervals of time, and generally on only a very few of the inhabitants of the same region at the same time. I further believe, that this very slow, intermittent action of natural selection accords perfectly well with what geology tells us of the rate and manner at which the inhabitants of this world have changed."

    The evolutionists rejected a core principle of evolution, but still maintained Darwin was right. It baffles me.

    "Evolutionary hypothesis predicts no biological outcomes."

    Again from Darwin: "But which groups will ultimately prevail, no man can predict; for we well know that many groups, formerly most extensively developed, have now become extinct."

    So they kept that piece. It makes sense, anything that can't be predicted can predict anything.

    "Given that the DNA variability under discussion is subtractive, not additive, there is no reason to think that the variations are not just subsets or subspecies of the main, overall species, which still exists."

    And this is another blow against Darwin's theory. For the first part he keeps insisting that variations selected will out preform the original species, effectively killing them off until only the better adapted new species exists. Since species like the Cichlids exist, this undermines another aspect.

    "here are distant stars which are just like our star but are at a distant point in their life cycle. The idea of Deep Time, of billions of years, explains so much of the world around us" - Nye

    Astronomy does not equal biology. Of course, Darwin pull the same stunt: "Natural selection can act only by the preservation and accumulation of infinitesimally small inherited modifications, each profitable to the preserved being; and as modern geology has almost banished such views as the excavation of a great valley by a single diluvial wave, so will natural selection, if it be a true principle, banish the belief of the continued creation of new organic beings, or of any great and sudden modification in their structure."

    They may have switched to new sheet music, but the song sounds the same.

  2. Hello everyone,

    It is not just biology, it is physics -astrophysics, geophysics- too. I just hope a paradigm shift should be about to come.

    This is an old site, but suppression of the dissent in science is still way too common nowadays.

    With the sadness in my heart, ironically, I'm so glad I'm not an academic science student.

    ArchiveFreedom Site

    Kind Regards.


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