Of all the facts in The Origin of Species, embryology was the most important in support of the theory. In a letter to Asa Gray in September 1860, Darwin wrote – “embryology is to me by far the strongest single class of facts in favor” of the theory.

Then, just two months before the release of the first edition of The Origin of Species in September 1859, Darwin wrote to Charles Lyell, “Embryology in Chapter VIII is one of my strongest points I think.”

Darwin was fascinated by embryology. Writing in his autobiography, Darwin recalls: “Hardly any point gave me so much satisfaction when I was at work on the Origin, as the explanation of the wide difference in many classes between the embryo and the adult animal.”

To the point, Darwin writes – “We have seen in the first chapter that the homological [similar] structure of man, his embryological development and the rudiments which he still retains, all declare in the plainest manner that he is descended from some lower form.”

Darwin along with Fritz Müller (1821–1897) and Ernest Haeckel (1834–1919) were following in the footstep of Karl Ernst von Baer (1792–1876). Baer promoted the concept that a species’ embryological development (ontogeny) retraces the species’ entire evolutionary development (phylogeny).

In the case of man, then, the human embryo begins as a single cell and is progressively transformed into a tadpole, then to a fish, to an amphibian, to a monkey, and finally to man. In other words, at the different stages of development, the embryo is actually a series of ancestor species. The sequences of the embryo retrace the steps of evolution. Haeckel coined this process with the now-famous phrase “ontogeny recapitulates phylogeny.”

In the case of the appendix, then, the rise and fall of the appendix should be seen in the human embryo to demonstrate our presumed evolutionary human ancestry—from a functional to a non-functional organ. The question is does the evidence match the theory? The answer is – NO.

The reasons why the answer is NO, include  

• The appendix is not consistently found throughout the animal kingdom, occurring in only a few diverse mammals
• Not until the fifth fetal week does the appendix begin to develop
• Only after the fifth fetal month does the proximal end start differentiate into the true caecum
• Maximum growth of the appendix does not occur until after birth when the neonate takes on essential bacteria to reside in its colon
• Lymphoid follicles do not appear in the appendix until two weeks after birth at the same time that colonization of the large bowel with bacteria.

Contrary to the theory, at no point in the development of the appendix in the human embryo does arise and decline into a vestige organ. Rebecca E. Fisher, Ph.D., Postdoctoral Fellow from the Center for Functional Anatomy & Evolution Johns Hopkins University School of Medicine, in a review article entitled “The primate appendix: A reassessment” concludes that “the evolutionary history of the appendix has also proven difficult to trace.”  

The evidence on the development of the appendix now clearly stands to demonstrate the utter fallacy of the long-standing “ontogeny recapitulates phylogeny” theory of evolution.

Jerry Coyne’s (2009) contention in Why Evolution is True that, “our appendix is simply the remnant of an organ that was critically important to our leaf-eating ancestors, but is of no real value to use” is another clear example of deception used in the promotion evolution. The evidence is clear: the appendix is not an evolutionary leftover.

The “vestige” status of the appendix originated with Charles Darwin in The Descent of Man (1871). In Chapter 1, Darwin writes -

“With respect to the alimentary canal I have met with an account of only a single rudiment [vestige], namely the vermiform appendage of the caecum… It appears as if, in consequence of changed diet or habits [disuse], the caecum had become much shortened in various animals, the vermiform appendage being left as a rudiment of the shortened part… Not only is it useless, but it is sometimes the cause of death”

Darwin’s concept of the appendix continued unchallenged until late in the twenteth century when clinical research began to demonstrate that not only does the appendix function to balance the bacteria in the gastrointestinal tract, the appendix plays an important immunological function. 

Loren G. Martin, professor of physiology at Oklahoma State University, stated in Scientific America -

“Among adult humans, the appendix is now thought to be involved primarily in immune functions. Lymphoid tissue begins to accumulate in the appendix shortly after birth and reaches a peak between the second and third decades of life, decreasing rapidly thereafter and practically disappearing after the age of 60. During the early years of development, however, the appendix has been shown to function as a lymphoid organ, assisting with the maturation of B lymphocytes (one variety of white blood cell) and in the production of the class of antibodies known as immunoglobulin A (IgA) antibodies. Researchers have also shown that the appendix is involved in the production of molecules that help to direct the movement of lymphocytes to various other locations in the body.”

Martin continues noting, “the function of the appendix appears to be to expose white blood cells to the wide variety of antigens, or foreign substances, present in the gastrointestinal tract. Thus, the appendix probably helps to suppress potentially destructive humoral (blood- and lymph-borne) antibody responses while promoting local immunity. The appendix–like the tiny structures called Peyer’s patches in other areas of the gastrointestinal tract–takes up antigens from the contents of the intestines and reacts to these contents. This local immune system plays a vital role in the physiological immune response and in the control of food, drug, microbial or viral antigens.”

Jerry Coyne (2009), professor at the University of Chicago, writes in his new book, Why Evolution is True that, “We humans have many vestigial features proving that we evolved. The most popular is the appendix.” Coyne claims that: “our appendix is simply the remnant of an organ that was critically important to our leaf-eating ancestors, but is of no real value to use.”

Classifying the appendix as “no real value” exemplifies how evolution adherents persist to be woodwinked by ideology. Mounting scientific evidence continues to demonstrate why evolution is NOT true.

Long denigrated as vestigial or useless structure, the human appendix is now known to have a number of specific functions. The most widely recognized function is as a “safe house” for the beneficial bacteria living in the human gut.” There are approximately 500 species of bacteria in the gut alone—the continued presence of beneficial bacteria is essential for good health.

ScienceDaily in an article entitled “Appendix Isn’t Useless At All: It’s A Safe House For Good Bacteria,” October 8, 2007, William Parker, Ph.D., assistant professor of experimental surgery along with R. Randal Bollinger, M.D., Ph.D., Duke University professor emeritus noted—”Our studies have indicated that the immune system protects and nourishes the colonies of microbes living in the biofilm. By protecting these good microbes, the harmful microbes have no place to locate. We have also shown that biofilms are most pronounced in the appendix and their prevalence decreases moving away from it.” One of the functions of the appendix is to serve as a microbe storehouse.

According to their study published in the Journal of Theoretical Biology, the bacteria in the human gut functions to digest food and produce vitamins, like Vitamin K—essential to coagulation. In the event that bacteria in the intestines become unbalanced, or taken over by opportunistic organisms such as cholera or amoebic dysentery, the appendix functions to reboot the bacterial flora. Parker explains the mechanism: “Once the bowel contents have left the body, the good bacteria hidden away in the appendix can emerge and repopulate the lining of the intestine before more harmful bacteria can take up residence.”

“Darwin simply didn’t have access to the information we have,” explains Parker. “If Darwin had been aware of the species that have an appendix attached to a large cecum… he probably would not have thought of the appendix as a vestige of evolution.”

When Jerry Coyne (2009), professor at the University of Chicago, writing in his book, Why Evolution is True that “our appendix is simply the remnant of an organ that was critically important to our leaf-eating ancestors, but is of no real value to use,” excluded known evidence. Continued adherence to the vestige status of the appendix by evolutionists requires rejection of the scientific method.

“Maybe it’s time to correct the textbooks,” says William Parker, Ph.D., assistant professor of surgical sciences at Duke and the senior author of the study. “Many biology texts today still refer to the appendix as a ‘vestigial organ.’”  

Jerry Coyne (2009), professor at the University of Chicago, writes in his new book, Why Evolution is True that, “We humans have many vestigial features proving that we evolved. The most popular is the appendix.” Coyne claims that: “our appendix is simply the remnant of an organ that was critically important to our leaf-eating ancestors, but is of no real value to use.”

Coyne believes the expansion of appendix development occurred because of “use” followed by contraction due to “disuse”—the rise and fall of the appendix. Following this belief, one would expect to find the appendix first increasing then decreasing in our presumed human evolutionary ancestors.

The vestige logic is great; unfortunately, the evidence does not support the logic. Coyne, along with the rest of the vestiges adherents fail mention that the rise and fall theory of the appendix simply never happened. The reason: the appendix occurs only in a few diverse mammals—and does not follow an evolutionary continum of rising and falling.

In fact, the appendix, in any form, is not present in any invertebrate. Among the vertebrates, the appendix is absent in fish, amphibians, reptiles, birds, and, most importantly, even in only a few mammals. In fact, the appendix is only present in a few marsupials, including the wombat and South American opossum, a few rodents, including rabbits and rats, and only a few primates, only the anthropoid apes and man. Even monkeys do not have an appendix.

Even though the appendix is “critically important to our leaf-eating ancestors,” tracing the development of the rise and fall of the appendix in presumed human evolutionary ancestors is simply a mirage—nothing more.

Although the Chimpanzee, touted as our closest genetic ancestor, has an appendix, surgeons are not exploring the possibility of any type of Chimpanzee-to-human transplantation and nor is the pharmaceutical industry exploring the use of any Chimpanzee molecules for use in humans, not even insulin.

Insulin and heart valves from the Suidae, the biological family to which pigs and their relatives belong, have long been used in humans. Calcitonin, a polypeptide hormone, is identical to the Calcitonin produced in the species of the fish family known as Salmonidae—Salmon. Why are pigs and the salmon more similar to humans than our closest genetic counterpart?  

The reason is—nature is discontinuous and digital, designed as unique creations. Anatomical and molecular evidence demonstrates that nature is not the result of “slight, successive changes” via mutations as touted by evolution adherents—evidence Jerry Coyne must inconveniently ignore; a practice popularized by Charles Darwin.  

In the final paragraph of the section entitled Rudimentary, Atrophied, and Aborted Organs, Darwin writes: “Finally, the several classes of facts which have been considered in this chapter, seem to me to proclaim so plainly, that the innumerable species, genera and families, with which this world is peopled, are all descended, each within its own class or group, from common parents, and have all been modified in the course of descent, that I should without hesitation adopt this view even if it were unsupported by other facts or arguments.”

The concept of vestiges from the actions of “use and disuse” continues today even though proven to be “unsupported by other facts or arguments.” Little wonder why students continue to question whether science in the classroom today is really science. Even though touted by esteemed college professors, what may be “most popular” can be dead wrong. 

Vestiges  are tauted as evidence for biological evolution based on the Larmarckian concept of “use and disuse” that Charles Darwin reluctantly, yet fully accepted by the 6^th edition of The Origin of Species in 1872.

In the 1^st edition Darwin wrote that“use and disuse seem to have produced some effect” that was later changed to “use and disuse seem to have produced a considerable effect” in the 6^th edition. For Darwin, the importance of “use and disuse” increased from “some effect” to “considerable effect.”

In this series, we are examining the concept that the human appendix is a vestige structure through the process of “disuse.” Vestiges are thought to be biological elements that have lost their function through “disuse.” At issue is—what is the evidence that the process of “disuse” can actually produce vestiges?

In the decade following the publication of the 6^th edition, German biologist August Weismann, at the University of Freiburg, launched the first scientific inquiry to directly challenging Darwin’s theory. Now known as the “Weisman Barrier” in 1883 Weismann cut off the tails of mice from twenty-one generations. Seeing that the twenty-second generation still had tails, Weismann concluded that the evidence contradicted Darwin’s theory of “disuse” and that despite obvious reasons for change in the mice, “continuity” was observed, not new variations.

The concept of the Weismann Barrier became central to the emerging  Modern evolutionary synthesis. “Disuse” alone simply does not result in vestige structures. Ernst Mayr, known as Darwin’s bulldog of the twenty-first century, called Weismann “the second most notable evolutionary theorist of the nineteenth century, after Charles Darwin.”

Evidence from the Weismann Barrier continues to stand unchallenged, now for over 100 years. Even more to the point, after thousands of years of circumcision, “disuse” has failed to any effect on human anatomy. Without scientific experimental evidence demonstrating that “disuse” can result in any biological changes, the concept of vestige as evidence for evolution remains untenetable.

Other known vestige problems for evolution include, 1) the appendix is not found systematically found through nature, even in mammals; 2) “vestige” structures are now known to be functional. These evolutionary contradictions for vestiges continue to undermining evidence for evolution.

In the up-coming posts, we will continue to explore why these last two problems have completely undermined the concept that the human appendix is a vestige structure.

Charles Darwin attempted to avoid the use of the term “vestiges” largely because the term had been associated with the “erroneous” Larmarckian concept of “use and disuse” that was only “veritable rubbish.”

Jean-Baptiste Lamarck (1744 – 1829) was a member of the French Academy of Sciences and was appointed to the Chair of Botany in 1788. When the Muséum national d’Histoire naturelle was founded in 1793, Lamarck was appointed professor of zoology. In 1801, he published Système des animaux sans vertèbres, a major work on the classifications and coined the term invertebrates. Lamarck is thought to be the first use the term biology in its modern sense. Lamarck continued his work as a premier authority on invertebrate zoology.

Darwin did credit “Lamarck as the first man whose conclusions on the subject excited much attention.… In these works he up holds the doctrine that all species, including man, are descended from other species.”

Lamarck’s theory of evolution, which he referred to as “transformism,” was based on the idea that individuals develop new traits during their own lifetimes by “use and disuse” and transmit them to the next generation. Larmack writes – “Progress in complexity of organization exhibits anomalies here and there in the general series of animals, due to the influence of environment and of acquired habits.”

The giraffe served as Lamarck’s classic example of evolution through “use,” acquiring longer necks in successive generations in competition to reach the ever-scarcer leaves higher in the trees. In illustrating Lamarck’s views on adaptation, Darwin wrote, “To this latter agency he seems to attribute all the beautiful adaptations in nature; such as the long neck of the giraffe for browsing on the branches of trees.”

For Darwin, however, this explanation was simply not scientific – “Lamarck, who believed in an innate and inevitable tendency towards perfection in all organic beings, seems to have felt this difficulty so strongly that he was led to suppose that new and simple forms are continually being produced by spontaneous generation. Science has not as yet proved the truth of this belief.”

One of the most eminent pre-Darwinists was Charles Darwin’s own grandfather, Erasmus Darwin (1731–1802). Erasmus discussed his ideas at length in a two-volume work, Zoonomia, published in 1794. Erasmus wrote that “all … have risen from one living filament.”

Erasmus’ book was widely popular in Western Europe- even translated into German, French, and Italian. Erasmus envisioned that the driving force behind species modification was a result of “lust, hunger, and danger.” In line with Greek philosophy, Erasmus envisioned changes by “continuing to improve its own inherent activity.”

Actually how these “improvements” developed was completely unknown to Lamarck and Erasmus—evolution was a philosophy, not a science. The unknown cause of “improvements” is what drove Darwin to discover the underlying laws of nature—scientifically. Writing in the preface of The Origin of Species, Darwin suggests how Erasmus’s work, although “erroneous,” may have influenced Lamarck: “It is curious how largely my grandfather, Dr. Erasmus Darwin, anticipated the views and erroneous grounds of opinion of Lamarck in his Zoonomia.”

For Lamarck, new characteristics are acquired through the process of “use and disuse.” Darwin’s grandfather, Erasmus Darwin, was a Lamarckian evolutionist. Charles Darwin, however, in pursuit of a “scientific theory” of evolution, initially opposed Lamarckian evolution, only granting the theory marginal support.

In a letter written to J. D. Hooker in 1844, Darwin wrote, “Heaven forefend me from Lamarck nonsense of a ‘tendency to progression.’ … But the conclusions I am led to are not widely diff erent from his, though the means of change are wholly so.” “With respect to books on this subject,” Darwin continues, “I do not know any systematic ones, except Lamarck’s, which is veritable rubbish.”

Although attempting to distance himself from Lamarck’s concepts of “use and disuse” and “vestages,” Darwin distain for “use and disuse” eventually waned as causes for the origin of variation required for the actions of natural selection remained Darwin’s largest unsumountable enigma.

Since then, the term, “vestiges” has once again gained prominence over “rudiments,” as has Larmarckian concepts of evolution. The question remains, however, are structures classified as “vestiges” evidence of evolution? Specifically, have vestiges seemingly lost all or most of their original function in a species through evolution?

To address answers to these questions, we will be examining the most popular example of vestiges—the mammalian appendix in the up-coming posts.   

In this first in a series, we will discover how structures labeled vestiges have played an important role as evidence for the theory of evolutionary. By the time The Origin of Species was published in 1859, vestiges had already been a hot topic. It was Robert Chambers in the publication of his book entitled Vestiges of the Natural History of Creation in 1844 that popularized the concept of vestiges. Chambers brought together various ideas of stellar evolution and progressive transmutation of species. The book was a best-seller is considered largely responsible for causing a shift in public opinion that paved the way for the general acceptance of evolution following the publication of  The Origin of Species.

While agreeing with the general concept of evolution, Darwin took many exceptions with Chamber’s perspective on vestiges and the concept that evolution occurs by sudden changes in nature. Darwin wrote – “The author [Chambers] apparently believes that organisation progresses by sudden leaps, but that the effects produced by the conditions of life are gradual.”

Perhaps because of these differences with Robert Chambers, Darwin even avoided defining the term “vestiges” in The Origin of Species. In the Glossary, however, Darwin defines a related term: “RUDIMENTARY.—Very imperfectly developed.” In The Origin of Species, the term “rudimentary” appears 101 times.

Darwin envisions rudimentary structures to be the result of two different dynamics: 1) as structures “imperfectly developed”—emerging, and 2) as structures in disuse undergoing loss of function—elimination. Darwin writes – “Rudimentary organs will speak infallibly with respect to the nature of long-lost structures”—a Lamarckian disuse concept. Darwin explains that rudimentary structures continue to exist because “natural selection… had no power to check deviations in their structure.”

Today however, only the process of elimination due to the disuse concept is thought to be in operation. WIKIPEDIA.org states: “Vestigiality describes homologous characters of organisms that have seemingly lost all or most of their original function in a species through evolution. Answers.com defines vestige structures, as “A rudimentary or degenerate, usually nonfunctioning, structure that is the remnant of an organ or part that was fully developed or functioning in a preceding generation or an earlier stage of development.”

 This takes us to the next question – why did Darwin largely attempt to avoid the term vestiages that was associated with the Larmarckian concept of use and disuse?

But what could the confusion be over? Here are some examples.  Charles Darwin wrote in The Origin of Species - “There is no logical impossibility in the acquirement of any conceivable degree of perfection through natural selection”. Coyne contradicts Darwin by stating – “natural selection does not yield perfection”. Over a trivial issue, confusion reigns over whether natural selection can or cannot produce perfection in nature.

Presumably, to show how easy the theory of evolution is to understand, Coyne features what he calls the six basics of evolution: “evolution, gradualism, speciation, common ancestry, natural selection, and nonselective mechanisms”. For Coyne, natural selection is not the exclusive driving force of evolution.

Niles Eldredge, evolutionary biologist and curator of the American Museum of Natural History, disagrees. Niles Eldredge, architect  and designer of the museum’s currently touring Darwin exhibit in the companion book Darwin, Discovering the Tree of Life (2005), credits Darwin with discovering the actions of natural selection—the essence of evolution: “When [Darwin] formulated the principle of natural selection, he had discovered the central process of evolution.”

Unlike Coyne, Eldredge envisions evolution acting exclusively through the process of natural selection: “A century and a half ago, Charles Darwin offered the world a single, simple scientific explanation for the diversity of life on Earth: evolution by natural selection.” Unlike Coynes six basics of evolution, Eldredge uses a VISTA acronym for natural selection that stands for Variation, Inheritance, Selection, Time, and Adaptation.

Differences in approach even between Coyne and Eldredge, exemplify why evolution theory continues to be confusing—even on the basics. The teaching of evolution is in chaos. Coyne pines “most of my university students who supposedly learned evolution in high school, come to my courses know almost nothing about this central organizing theory of biology.” Could it be because a unified theory of evolution simply does not exist?

Even university science major graduates seem to be no better. T. Ryan Gregory and Cameron A. J. Ellis, in their paper entitled “Conceptions of Evolution Among Science Graduate Students” published in BioScience 59(9):792-799 (2009), surprizingly found that less than 30% of students pursuing advanced science degrees could correctly identify even the basic principles of evolution.

The reason is—a comprehensive theory of evolution simply does not exist. Even with the convening of the most respected evolutionary scientists at the Altenberg Summit in 2008, no consensus was reached on a comprehensive theory of evolution.

Given the flood of available evidence, in the wake of Crick’s Central Dogma collapse, evolution is a theory that remains in chaos—now more than ever.

Species and natural selection are the two most common terms Charles Darwin uses in the book from the title—The Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life.

In the “Glossary of the Principle Scientific Terms Used in the Present Volume”, while Darwin defines “Organism” as “An organised being, whether plant or animal”, surprizingly, neither “species” nor “natural selection,” the key terms of the book, are defined in the Glossary. The question is why.

Defining “species” became one of Darwin’s great challenges. From the start, Darwin recognized that among naturalists of the day, the term “species” did not have a consistent definition: “No one definition has satisfied all naturalists; yet every naturalist knows vaguely what he means when he speaks of a species. Generally the term includes the unknown element of a distinct act of creation.”

 Unlike Newton who was able to measure and test the laws of gravity, Darwin had to deal with the problem that there “is no possible test but individual opinion to determine which of them shall be considered as species and which as varieties.”

In the pursuit for a definition, Darwin suggested that as a variety begins to exceed the number of the parent species, the new variety becomes a new species: “If a variety were to flourish so as to exceed in numbers the parent species, it would then rank as the species.” In other words, species was simply a numbers game.

Darwin’s numbers game approach was never seriously taken—even by Darwin himself. After 150 years, the problem of defining species has not been resolved and is now known as the long-standing “Species Problem.”

Jody Hey of Rutgers University wrote in Trends in Ecology & Evolution (2001) – “The species problem is the long-standing failure of biologists to agree on how we should identify species and how we should define the word ‘species’. The innumerable attacks on the problem have turned the often-repeated question ‘what are species?’ into a philosophical conundrum.”

Massimo Pigliucci professor of Ecology and Evolution at the State University of New York at Stony Brook noted in BioEssays (2003) “First, the species problem is not primarily an empirical one, but it is rather fraught with philosophical questions that require – but cannot be settled by – empirical evidence.”

The Origin of Species is loaded with plastic contradictory definitions even on the central term of the book—species. Darwin eventually concedes on the definition of species by writing – “We have seen that there is no infallible criterion by which to distinguish species and well-marked varieties.”

Today, known evidence remains compatible with the following definition of species that Darwin long endvoured to eliminate – “Generally the term [species] includes the unknown element of a distinct act of creation.”

Things that Darwin once found pleasurable as a young man turned on him. By 1865, at the age of fifty-six, Darwin summed up his problems in writing to a new medical adviser by writing that for twenty-five years he had experienced extreme flatulence, preceded by ringing ears and visual black dots, and vomiting preceded by shivering and crying.

In 1871, one year before the publication of the sixth and final edition of The Origin of Species, in a letter to his natural selection collegue, Alfred Wallace, Darwin confided: “present I feel sick of everything, and if I could occupy time and forget my daily discomforts, or rather miseries, I would never publish another word.”

Time and health took a toll on Darwin’s mind: “I have said that in one respect my mind has changed during the last twenty or thirty years. Up to the age of thirty, or beyond it, poetry of many kinds, such as the works of Milton, Gray, Byron, Wordsworth, Coleridge, and Shelley, gave me great pleasure, and even as a schoolboy I took intense delight in Shakespeare, especially in historical plays. But now after many years I cannot endure to read a line of poetry: I have tried lately to read Shakespeare, and found it so intolerably dull that it nauseated me. I have also lost my taste for pictures or music.”

What caused Darwin’s life-long health problems? To explain why Darwin experienced such poor health, scientists have pointed to a one night event east of the Andes near Mendoza in March 1835—Darwin wrote: “At night I experienced an attack (for it deserves no less a name) of the Vinchuca, a species of Reduvius, the great black bug of the Pampas. It is most disgusting to feel soft wingless insects, about an inch long, crawling over one’s body.” Darwin is thought to have been bitten by an insect called the “Great Black Bug of the Pampas” carrying the infectious parasite Trypanosoma cruzi.

For over a period of forty years, Darwin suffered intermittently from various combinations of symptoms such as malaise, vertigo, dizziness, muscle spasms and tremors, vomiting, cramps and colics, bloating and nocturnal intestinal gas, headaches, alterations of vision, severe tiredness, nervous exhaustion, dyspnea, skin problems such as blisters all over the scalp and eczema, crying, anxiety, sensation of impending death and loss of consciousness, fainting, tachycardia, insomnia, tinnitus, and depression. However, since attempts to test Darwin’s remains at the Westminster Abbey by using modern PCR techniques have been refused by the Abbey’s curator, the real cause of Darwin’s health problems remains only speculative.

For Charles Darwin, molecular clocks were the farthest his mind, not to mention cellular biology or DNA. In 1859, inheritance was thought to occur by blending the characteristics with the new information learned by the “gemmules” in the parents. Gregor Mendel, the Austrian monk, in 1865 eventually decimated blending inheritance, but the foundation of modern genetics went unrecognized until rediscovered by Hugo de Vries and Carl Correns in 1900.

To estimate the pace of evolution, in 1962 molecular biologist Emile Zuckerkandl and Nobel Prize winner Linus Pauling were working at California Institite of Technology on hemoglobin evolution and expressed the idea of “molecular anthropology” as a new discipline. The idea was later termed the molecular clock theory. The purpose of the molecular clock is to estimate the rate of evolution for individual molecules. In 1962, molecular sequence problems were just emerging.

Zuckerkandl and Pauling postulated that in a protein, each amino acid randomly changes at a constant rate. If the estimated time for divergence between species and the number of amino acid changes since that time can be determined from the fossil record, the rate of change can be calculated. This rate of molecular change (time per amino acid change) has been called the molecular clock.

As the molecular data began to accumulate during the early 1990s, it became increasingly apparent that the theory was intrinsically even more problematic when examining evolution from the context of the entire organism and the fossil record. At the core of Darwinian evolution are the successive, slight changes in molecules. However, how different molecules can evolve at different rates in the same organism emerged as an enigma.

Information from the molecular clock was once thought to be one of the most useful tools in establishing evolutionary biology. How the evolution of each molecule can run by a different molecular clock in the same organism continues to undermine a cohesive theory of molecular evolution.

The pursuit to resolve the clock issue has reemerged onto center stage because the rate of molecular change is foundational to evolution. If the molecular mechanisms of evolution cannot be traced, the only logical conclusion is that molecular biology has played no role in evolution.

In 2007, Naoyuki Takahata, of The Graduate University for Advanced Studies in Japan, wrote in the journal Genetics, “It is now clear that any kind of molecular clock ticks erratically, but it is nevertheless widely used [unfortunately] for estimating species divergence times.”

How Zuckerkandl and Pauling’s simple postulate has become so complicated begs the question, are molecular clocks real? Professor of evolutionary biology Thomas Cavalier-Smith of the University of Oxford in England wrote in Philosophical Transactions of the Royal Society B in a paper entitled Cell Evolution and Earth History: Stasis and Revolution that the answer is no: “Evolution is not evenly paced and there are no real molecular clocks.”

Available evidence bodes negatively for the usefulness of molecular clocks in establishing any shape for the Tree of Life. What was originally thought to become a cornerstone for molecular evolution is now irreconcilable with evolution and created chaos in evolutionary thought. Difficulties associated with attempting to explain how a family of homologous proteins could have evolved at constant rates have created chaos in evolutionary thought.

Rather than supporting the theory of evolution, the molecular clock evidence and the sequence data actually undermine the theory of evolution through “successive, slight” variations in molecular biology. Just as hope in the fossil record, the origin of life, and the sequence of amino acids dissipated, the hope that molecular clocks will become an evidential, evolutionary cornerstone is vaporizing. In 2005, geneticist Giuseppe Sermonti wrote: “Once the universal ‘molecular clock’ was shelved, biochemists ceased to question (in any case dubious) datings proposed by paleontologists.”

Molecular biologists beginning in the early twentieth century had expected to trace the organization of inorganic to organic molecules as well as the successive molecular changes as the species evolved. Clearly, however, the convergence of molecular evidence does not support the theory. Darwin concluded in The Origin of Species if the evidence does not support “numerous, successive, slight modifications, my theory would absolutely break down.”

Molecular clocks, as evidence for evolution, continue to be unsuccessful in delivering on earlier expectations.

While it is unknown how the 1,250 copies could have been sold on “the day of publication” without Amazon.com, what is known is that Darwin was famous long before the publication of the first edition of The Origin of Species in 1859.

Charles Darwin was following in the tradition of his grandfather, Erasmus Darwin—author of the infamous Zoönomia. King George III even asked Erasmus to be his doctor, but he refused the appointment—too busy.

Erasmus was building a vast network of associates that became known as the leading social and philosophical lights. With contacts like Matthew Boulton, Josiah Wedgwood, and James Watt, Erasmus established the Lunar Society that became the main intellectual powerhouse of the Industrial Revolution in England.

By the time Charles Darwin entered Edinburgh University, Zoönomia (meaning “the law of life” in Latin) had become a popular poetry and science textbook. At Edinburgh University, Charles Darwin learned that his professor, Robert Edmund Grant, quoted from Zoönomia for his doctoral thesis. 

Just months after returning from the voyage on the HMS Beagle in February 1837, and before starting working on what is now known as The Origin of Species, Darwin was elected to the Council of the Royal Geographical Society, later accepting Darwin accepted the position of Secretary of the Society in March 1838. Darwin was elected as a Fellow of the Royal Society in January 1839. The Geographic and Royal Society institutions were reserved for the intellectual elite—only.

The Darwin’s in the eighteenth century has been likened to the Kennedy’s of the nineteenth century. Darwin’s notoriety can even be seen at play during the voyage of the HMS Beagle. By British custom, the ship’s surgeon traditionally took the position of the official “naturalist.” Darwin’s role was to be a “gentleman’s naturalist” and assist the ship’s surgeon, Robert McKormick, and Captain FitzRoy. 

On shore in Brazil, however, it was the 22-year old Charles Darwin, not Doctor McKormick, who began receiving all the notoriety and the invitations from dignitaries on shore. Reasonably, McKormick felt upstaged by Darwin. Being sufficiently disgruntled, McKormick left the Beagle at Rio de Janeiro. McKormick’s status was “invalided out” back to Britain.

In 1859, not only was the topic of evolution was “in the air”, Darwin’s word was like E.F. Hutton speaking. The timing was perfect. Darwin’s pre-Origin notoriety preceded the successful launch of one the most influential and contentious books ever in the history of science.

In 1959, Spanish Catalan biochemist Joan Oró began to synthesize adenine, a key component of RNA and DNA, from hydrogen cyanide, similar to a Miller–Urey experiment. 

Like the Miller–Urey experiment though, the lack of geological evidence for hydrogen cyanide in the fossil record is missing. Another problem with hydrogen cyanide is that at room temperature, it becomes a gas toxic to cellular metabolism. During the German Nazi regime in the mid-twentieth century, hydrogen cyanide was used as an agent for mass murder.  

To date, not one laboratory experiment with realistic early Earth elements and conditions has produced a single nucleic acid. Scripps Research Institute biochemist Gerald Joyce states that the “most reasonable interpretation is that life did not start with RNA.” The origin of life is so difficult a problem that German researcher Kaus Dose stated in 1988 that the RNA theory is “a scheme of ignorance. Without fundamentally new insights in evolutionary processes … this ignorance is likely to persist.” 

In 1998, Leslie Orgel, senior research fellow and research professor at the Salk Institute for Biological Studies, where he directed the Chemical Evolution Laboratory, acknowledged that “we are very far from knowing whodunit” or what were the early environmental conditions on the Earth. 

Nearly twenty years later, the role of RNA in the origin of life remains elusive, if not improbable. In 2007, commenting in Proceedings of the National Academy of Sciences of the United States of America on a paper by Phillipp Baaske and Eugene V. Koonin, senior investigator, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, stated that while more is known about RNA, the evolutionary role of RNA has severe difficulties and “still is a hypothetical entity; … the evolutionary path to the translation systems remains essentially uncharted.”

Charles Darwin in a letter Joseph Hooker in February 1871 speculated that life might have originated in “some warm little pond, with all sorts of ammonia and phosphoric salts, light, heat, electricity, &c., present, that a proteine compound was chemically formed ready to undergo still more complex changes”.

Darwin’s speculation went untested until the Miller–Urey experiment in 1952 at the University of Chicago. Stanley Miller and Harold Urey successfully produced some of Darwin’s “proteine compounds” by building on Alexander Oparin’s and J. B. S. Haldane’s hypothesis that the primitive conditions on Earth were favorable to the chemical reactions that synthesized organic compounds from inorganic precursors. Oparian and Haldane’s favorable conditions required a nitrogen-rich reducing atmosphere without oxygen.

The Miller-Urey experiment advanced the question to center stage—were the conditions of primitive Earth the same as proposed by Oparin and Haldane? Was early Earth nitrogen-rich? Was oxygen absent?

Since 1952, research on the actual chemical conditions of the primitive Earth has been on the investigative frontlines of origin of life research. After over 50 years, the consensus is inconclusive. Wikipedia, under the topic of “Origin of Life” in, now more commonly referred to as “Abiogenesis,” concludes: “There is no truly ‘standard model’ of the origin of life. Most currently accepted models draw at least some elements from the framework laid out by the Oparin-Haldane hypothesis.”

Irrespective of primitive Earth conditions, an even more challenging question emerges—what is the statisitcal probability for functional proteins to arise de novo from the “prebiotic soup” of amino acids by chance? 

Stephen Meyer, in his new book entitled Signature in the Cell, reviews the extensive research into answering this daunting question on chance. Based on the works of Robert Sauer at MIT, Douglas Axe at Cambridge University, and British cosmologist Sir Fred Hoyle, Meyer, concldues that “the improbability of generating the necessary proteins by chance—or the genetic information to produce them—to balloon beyond comprehension.”

Meyer writes, “The odds of getting even one functional protein of modest length (150 amino acids) by chance from a prebioitc soup is no better than 1 chance in 10¹⁶⁴.” Meyer continues, “Another way to say that is the probability of finding a functional protein by chance alone is a trillion, trillion, trillion, trillion, trillion, trillion, trillion, trillion times smaller than the odds of finding a single specific particle among all the particles in the universe.”

The evidence for the probability of origin of life arising from Darwin’s “warm little pond” seems to have vanished beyond the realm of any possibility—regardless of any early Earth scenario.

Darwin’s preamble to the first edition of The Origin of Species includes quotations from William Whewell’s popular book entitled Bridgewater Treatise and Francis Bacon’s sentential work entitled Advancement of Learning. From different worldview, both Whewell and Bacon advocated the use of inductive reasoning—the scientific method.

 Bacon (January 1561 – April 1626) is noted as one of the founders of the Scientific Revolution that eventually lead to the establishment of the Royal Society by Charles II in 1660. Whewell, one of Darwin’s dons at Cambridge University, is credited for coining the term “scientist.” 

Taking a comprehensive approach to the study of evolution, Darwin presented the two different worldviews of Bacon and Whewell. Whewell, envisioning nature apart from a “Divine” intervention,

“But with regard to the material world, we can at least go so far as this-we can perceive that events are brought about not by insulated interpositions of Divine power, exerted in each particular case, but by the establishment of general laws.”

Bacon, by contrast, envisioned nature as part of “God’s work,”

“To conclude, therefore, let no man out of a weak conceit of sobriety, or an ill-applied moderation, think or maintain, that a man can search too far or be too well studied in the book of God’s word, or in the book of God’s works; divinity or philosophy; but rather let men endeavour an endless progress or proficience in both.”

Darwin teaches, by example, to embrace the exploration of diverse worldviews. Modern education should take Darwin’s approach and “teach the controversy.”

Just two months before the release of the first edition of The Origin of Species in September 1859, Darwin wrote to Charles Lyell, “Embryology in Chapter VIII is one of my strongest points I think.”

Writing in his autobiography, Darwin recalls: “Hardly any point gave me so much satisfaction when I was at work on the Origin, as the explanation of the wide difference in many classes between the embryo and the adult animal.”

Darwin’s premise was that the similarity between the structure and the embryo of animal and man was primary proof that man evolved from animals. In The Descent of Man, published in 1871, Darwin writes in the first chapter that embryology provides the “ample and conclusive evidence in favour of the principle of gradual evolution.”

Darwin was not an embryologist, and instead relied on the work of others. In The Origin of Species, Darwin gave credit to Ernst Haeckel: “Professor Haeckel in his “Generelle Morphologie” and in [other] works has recently brought his great knowledge and abilities to bear on what he calls phylogeny, or the lines of descent of all organic beings. In drawing up the several series he trusts chiefly to embryological characters [to establish evolutionary sequences].”

Based on what Darwin thought was scientific evidence concluded: “So again it is probable, from what we know of the embryos of mammals, birds, fishes, and reptiles, that these animals are the modified descendants of some ancient progenitor.”

In The Origin of Species, Darwin wrote, “Thus, as it seems to me, the leading facts in embryology, which are second to none in importance, are explained on the principles of variation in the many descendants from some … ancient progenitor”

During the twentieth-century, Haeckel’s embryos were prominently displayed in nearly every biology textbook, even though Haeckel eventually confessed that the drawings were fraudulent.

In January 1909, Haeckel’s confession was published as a letter in the Munchener Allegemeine Zeitung, an international weekly publication for the sciences, arts, and technology. In the letter, Haeckel clearly states that the drawings were contrived by “comparative synthesis” and not by accurate reproduction. Without the fraud, the expected evolutionary embryonic sequences had obvious gaps. Haeckel concedes, “a small portion of my embryo pictures (possibly 6 or 8 in a hundred) are really ‘falsified’.”

Even more sadly, Haeckel’s only defense was that fraudulent practices were an accepted practice even by some of the “most esteemed biologists” of the day. Haeckel wrote, “After this compromising confession of ‘forgery’ I should be obliged to consider myself condemned and annihilated if I had not the consolation of seeing side by side with me in the prisoner’s dock hundreds of fellow culprits, among them many of the most trusted observers and most esteemed biologists. The great majority of all the diagrams in the best biological textbooks, treatises, and journals would incur in the same degree the charge of ‘forgery,’ for all of them are inexact, and are more or less doctored, schematised, and constructed.” Indeed the scientific method had been abandoned not only by Darwin and Haeckel, but also by a large segment of the profession of biology.

Paul R. Ehrlich of Stanford University and author of the famous overpopulation book, The Population Bomb, wrote in 1963 that Haeckel’s law now only has a leading role in mythology—not in science. “This generalization was originally called the biogenetic law by Haeckel and is often stated as ‘ontogeny recapitulates phylogeny.’ This crude interpretation of embryological sequences will not stand close examination, however. Its shortcomings have been almost universally pointed out by modern authors, but the idea still has a prominent place in biological mythology.”

Like Haeckel’s embryo drawings, the history of evolution  has been laced with an insidious legacy of fraud.

Darwin theorized natural selection to act through “slight, successive” changes -

“I do believe that natural selection will generally act very slowly, only over long periods of time…. natural selection acts slowly by accumulating slight, successive, favorable variations, it can produce no great or sudden modifications; it can act only by short and slow steps.”                                                            

While speculation on metabolic rates was beyond the scope of nineteenth century scientists, investigation in this field is now yielding new information on potential evolutionary correlates. During evolution, the continued increase in size and complexity, for example from “mouse-to-elephant”, was expected to follow corresponding “slight, successive” changes in basal metabolic rates in relationship to body mass.

The scientific team at The University of Birmingham in the United Kingdom headed by Craig White noted that the evolutionary “relationship between the basal metabolic rate (BMR) and body mass (M) of mammals has been at issue for almost seven decades.” BMR is a calculated number based on the equation BMR = aM^b and the exponent b has long been disputed. The universality of exponent b is at the center of investigation.

To determine the exponent b, the researchers studied high-quality BMR data from 585 species and a subset of 537 species and published their findings in the October 2009 edition of Evolution* entitled “Phylogenetically informed analysis of the allometry of Mammalian Basal metabolic rate supports neither geometric nor quarter-power scaling”. The team results re-establish the fact that no evolutionary relationship exists between BMR and M concluding –

“Thus, we conclude that no single value of b adequately characterizes the allometric relationship between body mass and BMR.”

Sherman J Sutter, writing for Science in the abstract entitled “Evolution: No b to Rule Them All”, concluded that -

“Their results reinforce doubts as to the existence of a universal allometric relationship between mammalian BMR and body mass.”

Evidence for the natural law of evolution through “slight, successive” changes in the BMR, as expected from Darwin’s theory of natural selection simply does not exist. Species are unique—“kind after kind.”

Evolution. 2009 Oct;63(10):2658-67.

In 1943, published in a paper entitled “Mutations of Bacteria from Virus Sensitivity to Virus Resistance,” microbiologist Salvador Luria, biophysicist Max Delbrück, and bacteriologist and geneticist Alfred Hershey discovered that mutations occur at a constant rate. In 1969, they were awarded the Nobel Prize in Physiology and Medicine “for their discoveries concerning the replication mechanism and genetic structure of virus.”

The Luria-Delbrück Experiment opened the question, are mutations inherent to microbes for the purpose of adaption to rapidly changinging environments and not for evolution? While microbe resistance through mutation is a logical mechanism for evolution, the reality is the bacteria have remained a bacteria and the virus has remained a virus. Preexistent genetic variants determine the range of mutations. Pierre-Paul Grassé, president of the French Academy of Sciences, observed, “bacteria, the study of which has formed a great part of the foundation of genetics and molecular biology … stabilized a billion years ago.”

The question is whether the mutations are the “raw material for evolution” or nature’s means for the microbes to adapt to the environment. In a 2009 review article by entitled “Darwinian evolution in the light of genomics”, published in Nucleic Acid Research, Eugene V Koonin concluded, “There is no consistent tendency of evolution towards increased genomic complexity” through mutation as expected with current evolutionary theories. Mechanisms of evolution remain beyond any known natural law.

Reflecting on the role of mutations, Grassé questioned, “What is the use of their unceasing mutations if they do not change?” Grassé concludes, “the mutations of bacteria and viruses are merely hereditary fluctuations around a median position; a swing to the right, a swing to the left, but no final evolutionary effect.” Microbes undergo constant mutations, but do not evolve – mutation stasis.

*Nucleic Acids Res. 2009 March; 37(4): 1011–1034 

The etymology of pangenesis comes from the Greek words pan (a prefix meaning “whole”, “encompassing”) and genesis (birth) or genos (origin). Gemmules were thought to learn from experiences.

The origin of new variations was critical for Darwin’s theory since the “slight, successive” changes in evolution requires a constant stream of new variations for the actions of natural selection. Gemmules were imagined particles. These learned gemmules particles sent from every cell (pan) in the body with new variations (genos) accumulated in the germ cells and had a ‘vote’ in the constitution of the offspring (genesis).

This hypothesis provided a possible mechanism for the inheritance of acquired characteristics, as proposed by Jean-Baptiste Lamarck, which Darwin believed to be the origin of new variations in living organisms.

Little did Darwin know that even before the publication of the fourth edition of The Origin of Species in 1866, Gregor Mendel had presented the now-famous paper entitled “Experiments on Plant Hybridization,” laying the foundations of modern genetics.

Although, Mendel’s discovery went unnoticed until the turn of the twentieth century, German biologist August Weismann, at the University of Freiburg, launched the first scientific evidence directly challenging Darwin’s theory. Now known as the “Weisman Barrier,” in 1883, Weismann cut off the tails of mice from 21 generations. Seeing that the 22^nd generation still had tails, Weismann concluded that the evidence contradicted Darwin’s theory of pangenesis despite obvious reasons for change in the mice, “continuity” was observed, not new variations.

Ernst Mayr, Darwin’s twentieth-century bull-dag, stated Weismann as “The second most notable evolutionary theorist of the 19th century.” What is still unresolved now 150 years later is—what is the origin of variation?

Genomics offers unprecedented opportunities for testing the central tenets of evolutionary biology formulated by Charles Darwin in The Origin of Species in 1859, later modified into the Central Dogma by the Modern Synthesis during the twentieth century.

In a 2009 review article by entitled “Darwinian evolution in the light of genomics”, published in Nucleic Acid Research, Eugene V Koonin concludes “[m]ajor contributions of horizonal gene transfer… undermine the Tree of Life concept. An adequate depiction of evolution requires the more complex concept of a network or ‘forest’ of life.” 

Darwin wrote in The Origin of Species,“[a]lthough the belief that an organ so perfect as the eye could have been formed by natural selection, is enough to stagger any one; yet in the case of any organ, if we know of a long series of gradations in complexity, each good for its possessor, then under changing conditions of life, there is no logical impossibility in the acquirement of any conceivable degree of perfection through natural selection.”

Koonin continues, “[t]here is no consistent tendency of evolution towards increased genomic complexity.” Genomics has failed to demostrate increasing complexity as hypothesized by Darwin.

Evolution needs to synthesis a new mechanism to survive. To this end, Koonin suggests the possibility: “a new synthesis of evolutionary biology might become feasible in a not so remote future.” Until then, genomic evidence fails to support evolution.

Koonin, EV. 2009. Darwinian evolution in the light of genomics. Nucleic Acid Research, 37(4)1011-1034.