In fact, Darwin abandoned the scientific method and declared that his theory of evolution was based on speculation –

I am quite conscious that my speculations run quite beyond the bounds of true science.

Darwin ascribed to the popular nineteenth century theory of blending genetics of inheritance in which the new generation was simply an averaging of the previous generations. Blending genetics was debunked by a contemporary of Darwin, an Austrian monk.

Just a few years after the publication of the first edition of The Origin of Species, Gregor Mendel, now known as the father of modern genetics, using the scientific method published his landmark paper on genetic inheritance. Mendel in studying the genetics of the pea plant discovered that the theory blending inheritance was wrong.

Mendel’s findings were intensely criticized. It was not until the turn of the twentieth century that the significance of Mendel’s findings was appreciated. Mendel was the Vincent van Gogh of modern genetics.

Mendel’s laws of genetics eventually became the foundation of the Modern Synthesis theory of evolution developed during the twentieth century. The central dogma of the Modern Synthesis theory is based on an accumulation of genetic mutations passed on to the next generation through natural selection.

At the core of the theory was Darwin’s concept of “slight, successive” evolutionary changes. The Modern Synthesis was the central unifying theory for the evolution industry during the early twentieth century. The discovery of the DNA molecule structure by Francis Crick and James Watson in 1953 sealed a place for the Modern Synthesis theory with a molecular mechanism for evolution.

DNA was discovered to be a double helix structure composed of a sequence of nucleic acids. The sequence was thought to be the information source driving the code of biological life and evolution.

While the technology was not available to study genetic mutational changes, at the time, the hunt was on to discover the evidence for “slight, successive” genetic mutation changes in the sequence of nucleic acids found in the DNA and RNA molecule as evidence for evolution.

This past week, an international team of scientists lead by David Brawand of the Center for Integrative Genomics at the University of Lausanne in Switzerland published their work in the journal Nature. In the paper, “The Evolution of Gene Expression Levels in Mammalian Organs”, reported “the sequencing of polyadenylated RNA from six organs across ten species that represent all major mammalian lineages (placentals, marsupials and monotremes) and birds (the evolutionary outgroup), with the goal of understanding the dynamics of mammalian transcriptome evolution.”

The underlying purpose was of Brawand’s investigation was to demonstrate Darwin’s “slight, successive” changes in gene expression across a mammalian lineages. Amazingly, however, the investigators failed to discover any evidence for the expected progressive “slight, successive” evolutionary changes in gene sequences between mammals.

While the team reported “that the rate of gene expression evolution varies among organs, lineages and chromosomes”, the glaring problem for evolution is the failure to discover a progression of “slight, successive” evolutionary changes in gene sequences between mammals. Genes varying at different rates fails is compatible with a mosaic pattern of life, a pattern indistinguishable from a design theory of life. The scientific evidence points to the fact that life is a mosaic, not a pattern of “slight, successive” evolutionary changes forming Darwin’s Tree of Life.

Reflecting on the deepening theory of evolution crisis, as early as 1998, the distinguished professor of evolution at the State University of New York at Stony Brook, Douglas Futuyma opined: “Like most scientific theories, evolutionary theory is incomplete in several respects, most conspicuously in that… it lacks a sufficient body of principles for translating between genes and phenotypes.” In other words, the genetics alone cannot not differentiate between species−phenotypes.

In 2005, Sean B Carroll, Professor of Molecular Biology, Genetics, and Medical Genetics at the University of Wisconsin agrees with Futuyma:

The Modern Synthesis established much of the foundation for how evolutionary biology has been discussed and taught for the past sixty years. However, despite the monikers of ‘Modern’ and ‘Synthesis’, it is incomplete.

As scientific molecular evidence continues to accumulate, the Modern Synthesis theory of evolution is emerging more as a mirage than a mechanism.  In facing the reality, Alan Love of the University of Minnesota concluded

My account also meshes with the recognition that a fully unified view of evolutionary processes may be out of reach.

While the theory of evolution was once in crisis, now the concept of evolution is in crisis without even a theory.

Since steroid hormones are known to perform sophisticated regulatory functions in microbes to man, the path of steroid evolution has entered center stage in the realm of investigative molecular biology.

Steroids hormones were first discovered in the mid-twentieth century by American chemist Edward Calvin Kendall while working at the Mayo Clinic. In 1950, Kendall and colleague Philip Hench, along with Swiss chemist Tadeus Reichstein were awarded the Nobel Prize in Physiology or Medicine for “their discoveries relating to the hormones of the adrenal cortex, their structure and biological effects.”

The action of steroids occurs by attaching to specific receptor sites. Steroids act like a socket wrench on a bolt−a wrench that is only useful when aligned on the right sized bolt.

Corticosteroids are a class of steroids found in vertebrates.  One of the corticosteroid classes are the glucocorticoids. Glucocorticoids (glucose + cortex + steroid) are essential for life, acting to regulate and support a range of important cardiovascular, metabolic, immunologic, and homeostatic functions.

This past June, evolutionary biologist Sean Carroll and colleagues in the journal PLoS Genetics published a paper entitled “Mechanisms for the Evolution of a Derived Function in the Ancestral Glucocorticoid Receptor”.

Using site-directed mutagenesis, X-ray crystallography, and computational analyses of protein stability to recapitulate and determine the effects of historical mutations, Carroll investigated a range of potential pathways for the evolution of ancestral steroid receptors by genetic mutations to the glucocorticoid receptor in vertebrates.

Carroll suggests that the evolution of the vertebrate glucocorticoid receptor from an ancestral receptor type likely required three specific genetic mutations. Surprisingly, two of the mutations, while maintaining function individually, actually inactivates the receptor. The third mutation simply neutralizes the inactivation effect of the two previous mutations.

“The combined effect of these mutations is so strong that a third mutation, apparently neutral in the ancestral background,” Carroll explains, “evolved to buffer their degenerative effects.”

Assuming these two dysfunctional mutation followed by a neutralizing genetic mutation did occur, what is the probability that this series of events occurred by chance alone?

In “The Blind Watchmaker: Why the Evidence of Evolution Reveals a Universe without Design”, evolutionary biologist Richard Dawkins contends that evolution proceeds blindly without direction−evolution is like a blind watchmaker. Dawkins wagers on chance.  Darwin disagrees: “Mere chance, as we may call it, might cause one variety to differ in some character from its parents …, but this alone would never account for so habitual and large a degree of difference as that between the species of the same genus.”

The evidence, however, favors Darwin’s contention−not Dawkins.  Doug Axe, Director of the Biologic Institute, and molecular geneticist Ann Gauger in the paper “The Evolutionary Accessibility of New Enzymes Functions: A Case Study from the Biotin Pathway” demonstrated that for the conversion of one functional molecule to another requires a minimum of seven genetic mutations.  Based on a realistic population genetics model, Axe and Gauger demonstrated that each mutation would require 10²⁷ years. That’s a ten followed by 27 zeros.

The question is what is the chance of converting one functional molecule to another? Assuming that the estimated age of the universe is 13 billion years−that’s 13,000,000,000 (13 followed by 9 zeros), the time required to convert Carroll’s ancestral receptor to a vertebrate glucocorticoid receptor exceeds the time limits of the universe. Carroll, of course, did not consider time limitations. The probable role of chance, contrary to Dawkin’s earlier presumption, far exceeds the time limits of the universe.

These time constraints on evolution by genetic mutations are just one of the reasons why evolutionary scientists have largely abandoned the Modern Synthesis theory of evolution originally developed during the twentieth century following the discovery of the double-helix structure of DNA.

The 2008 Altenberg Summit hosted by Massimo Pigliucci of Stony Brook University and Gerd B Műller of University of Vienna. The sixteen evolutionary attendees of the summit, while dismissing the Modern Synthesis, proposed a series of new theoretical frameworks for evolution.

While Carroll’s approach to solving theoretical evolutionary problems was noble, evolution through genetic mutations is no longer the leading theory of evolution. Currently, the problem in evolution circles today is that disbanded Modern Synthesis theory of evolution has not been replaced by another unifying theory of evolution. Evolution, the Extended Synthesis published by MIT Press discusses alternatives to the Modern Synthesis.

Italian geneticist Giuseppe Sermonti succinctly summed up the problem with evolution: “There never really has been a scientific theory of evolution.”

Currently, a cohesive theory of evolution does not exist. Carroll’s recent experiments further highlights why genetic mutations are no longer considered a viable mechanism for biological evolution.

In fact, the discovery was a problem since the Neanderthal skulls are larger than human skulls. Darwin had argued that the advancement of evolution proceeded through “slight, successive changes”.

The Neanderthal fossils created a dilemma for Darwin, how could a larger brain precede a smaller brain? Darwin cautiously noted, that “it must be admitted that some skulls of very high antiquity, such as the famous one of Neanderthal, are well developed and capacious [large]”. For Darwin, the Neanderthal skulls were too large to have preceded humans.

As the fossil evidence for the Neanderthals continued to be discovered throughout Europe, the evidence seemed to point to the Neanderthals as a big game hunter transitional species leading to humans. With the goal of discovering our human evolutionary ancestors, the possibility that the Neanderthals represented a previously unknown ethnic group of humans was marginalized within the evolution industry.

During the twentieth century, at stake is whether the Neanderthals are a transitional species different from modern humans, or simply a human ethnic group.

Darwin, as we know now, was right to be cautious. Technology is answering the question. Just last year, a team lead by Svante Pääbo of the Department of Evolutionary Genetics at the Max-Planck Institute for Evolutionary Anthropology in Germany eroded the genetic difference between the Neanderthals and modern humans after publishing the full Neanderthal genome.

Commenting on the findings, John Hawks, assistant professor of anthropology at the University of Wisconsin, told BBC News that “They’re us. We’re them.”

“[T]he really surprising thing for many of us,” noted Professor Chris Stringer, research leader in human origins at London’s Natural History Museum, “is the implication that there has been some interbreeding between Neanderthals and modern humans in the past.” Since different species cannot interbreed, the Neanderthals can no longer be considered a transitional species.

Gregory Hannon of Cold Spring Harbor Laboratory in Laurel Hollow in New York concluded that the “publication of the full Neanderthal genome is a watershed event, a major historical achievement.” Genetic evidence is clear−the Neanderthals are not genetically distinct from modern humans.

This past week, Bruce L. Hardy of Kenyon College in Ohio and Marie-Hélène Moncel of the Muséum National d’Histoire Naturelle in Paris has further eroded the differences between the Neanderthals and modern Humans using anthropological evidence.

In the journal PLoS ONE this past week, Hardy and Moncel in the article “Neanderthal Use of Fish, Mammals, Birds, Starchy Plants and Wood 125-250,000 Years Ago”, further dispels anthropological differences between the Neanderthals and Humans.

Hardy and Moncel dispels the Neanderthal big game hunter myth: the “Neanderthals are most often portrayed as big game hunters who derived the vast majority of their diet from large terrestrial herbivores while birds, fish and plants are seen as relatively unimportant or beyond the capabilities of Neanderthals.”

At the fossil site in Payre, France, after evaluating 182 Neanderthal plant, fish and bird processing tools based in the wear and adhering biological residues on the tools, Hardy and Moncel  concluded that contrary to the once popular big game hunted paradigm, the Neanderthal diet “was quite diverse, including plants, large and small animals, fish, and possibly birds.”

“Neanderthals practiced what has been considered exclusively modern human behavior”,  Hardy and Moncel concluded. In other words, the diet of the Neanderthal is not different from modern Human.

These discoveries using previously unknown technologies continue to erode the differences rather than supporting the concept that the Neanderthals are an ancestral transitional link to human. The evolution industry is now tasked with discovering a better potential ancestral transitional link to humans.

“I hear your mom was asking about evolution,” Perry said. “That’s a theory that is out there — and it’s got some gaps in it.”

Writing in The Guardian, an original supported of Charles Darwin’s theory of evolution starting in the nineteenth century, liberal commentator Paul Krugman in his column, The Observer, ran crazy with the comment in the article entitled “The Republicans are now the anti-science party, on climate change and evolution, the party’s presidential hopefuls are wilfully ignorant.”

“Mr Perry, the governor of Texas,” according to Krugman, “recently made headlines by dismissing evolution as just a theory’, one that has “got some gaps in it”, an observation that will come as news to the vast majority of biologists.” Really?

Apparently, Krugman is “wilfully ignorant” about the “majority of biologists”. The book, Evolution-the Extended Synthesis published by MIT Press explains in detail why the “gaps” in evolution theory still persist.

The Evolution-the Extended Synthesis was written by sixteen leading scientists from around the world that met in Altenberg, Austria during the summer of 2008. The purpose of the meeting was to develop a new unifying and comprehensive theory of evolution to eliminate the “gaps” as mentioned by Perry. This meeting has been since been popularly called the Altenberg-16 Summit.

What emerged from the summit meeting, ironically, were sixteen different theories rather than a one unifying and comprehensive theory. Today, amazingly there are more “gaps” in the theory  of evolution than at any time since the publication of The Origin of Species by Darwin in 1859.

Kruger, apparently, is not aware of the controversies with the evolution of theories over the past 150 years, including Darwinism, neo-Darwinism, and the Modern Evolutionary Synthesis. No theory, to date, has arisen as an adequate unifying candidate to account for presumed evolution. Today, the field of evolution not only has gaps”, evolution is simply a philosophy without a scientific theory.

Ann Coulter was quick to jump into the debate with the blog posted on Human Events. However, unlike Kruger, Coulter in the post entitled “Liberals’ View of Darwin Unable to Evolve” on August 31^st with substance rather than typical extinct rhetoric produced by the government financed evolution industry.

From the genetic evidence, Coulter points out that scientist now recognize that “the vast majority of mutations are deleterious to the organism.” Krugman, apparently, is “wilfully  ignorant” that mutations, the foundation of the Modern Evolutionary Synthesis theory, have been abandoned as a theoretical mechanism for evolution.

Damaged genetic data cannot pave a road to progressively greater complexity as once anticipated by genetic evolutionists during the twentieth century.

As Coulter notes, not only do evolutionists have a problem with the Modern Evolutionary Synthesis theory, they have problem with the fossil record: “We also ought to find a colossal number of transitional organisms in the fossil record — for example, a squirrel on its way to becoming a bat, or a bear becoming a whale,” “But that’s not what the fossil record shows. We don’t have fossils for any intermediate creatures in the process of evolving into something better. This is why the late Stephen Jay Gould of Harvard referred to the absence of transitional fossils as the ‘trade secret’ of paleontology.” Krugman, apparently, is “wilfully ignorant” that the fossil record is a problem, not a solution, for the evolution industry.

How did evolutionists end up with a problem rather than a viable theory? Coulter explains: “Darwinists start with a theory and then rearrange the evidence.” Krugman, apparently, is “wilfully ignorant” that starting with Darwin,
the evolution industry has long since abandoned the scientific method. After the sparring, the obvious fact emerges, Krugman, not the Republicans, represent news media “anti-science” journalism.

Never has a theory played such leverage in a national presidential election campaign. Perhaps, Coulter is wrong - the Krugman camp is evolving into extinction.

Go campaign 2012.

When the platypus, nicknamed the “watermole,” was first discovered in 1797 by early European settlers near the Hawkesbury River, outside Sydney, it triggered a lasting controversy. The perplexed local governor, Captain John Hunter, sent specimens back to Mother England for study.

The “watermole” was equally mystifying in England. Zoologists George Shaw suggested it was a “freak imposture” sold to gullible seamen by Chinese taxidermists. Suspecting fraud, they tried to pry the “duck’s bill” off of the pelt, leaving marks on the bill that are still visible today at the British Museum in London.

In 1802, an English scientist confirmed that the creature was neither freak nor fraud, and he labeled the specimen “platypus” because of its flat bill and gave it the scientific name Ornithorhynchus anatinus. Since then, the platypus has stood as an iconic conundrum in natural history.

While voyaging on the HMS Beagle in 1836, Charles Darwin recorded his encounter with a platypus, during his travels along Coxs River near the Wolgan Valley in Australia:

In the dusk of the evening I took a stroll along a chain of ponds, which in this dry country represented the course of a river, and had the good fortune to see several of the famous Ornithorhynchus paradoxus. They were diving and playing about the surface of the water, but showed so little of their bodies, that they might easily have been mistaken for water-rats. Mr. Browne shot one.

At the time,  the Platypus official name was Ornithorhynchus paradoxus due to the paradoxical evolutionary status by Johann Blumenbach in 1800 then, later changed to Ornithorhynchus anatinus in 1934 to avoid the evolution controversy.

Not only do these furry animals actually lay eggs like a bird, the young feed on breast milk like a mammal and make venom like a snake. Although the platypus has been an evolutionary conundrum, the structure of the platypus genome has now been deciphered. In comparing the platypus genome with genomes of the human, mouse, dog, opossum, and chicken, researchers found that the platypus shares 82 percent of its genes with these animals.

For egg production, the platypus genome matches for the ZPAX genes that had previously been found only in birds, amphibians, and fish, and it shares with the chicken a gene for a type of egg-yolk protein called “vitellogenin.” For breast milk production, the platypus has genes for the family of milk proteins called caseins, which map together in a cluster matching humans. Lastly, the male platypus has spurs on its hind legs loaded with lethal venom, rising from duplicate reptilian-like genes.

The platypus exemplifies how similar genes in different species produce the same function. The question is how does genetic identification clarify the evolutionary place of the platypus? The answer is it does not.

According to Richard Gibb, Director of the Human Genome Sequencing Center at Baylor College of Medicine in Texas, concluded, “there is nothing quite as enigmatic as a platypus. You have got these reptilian repeat patterns and these more recently evolved milk genes and independent evolution of the venom. It all points to how idiosyncratic evolution is.”

Darwin proposed in The Origin of Species that as new species arise through “successive, slight changes,” there is corresponding extinction. Darwin wrote “extinction and natural selection go hand in hand.” The evidence however points to the conservation, not the extinction of variations.

A team led by Gregory Hannon of Cold Spring Harbor Laboratory in New York sequenced microRNAs, which regulate gene expression, from six platypus tissues, and also found a mix of reptile and mammal similarities, concluding that we “have microRNAs that are shared with chickens and not mammals as well as ones that are shared with mammals, but not chickens.

Classifying the platypus into an evolutionary paradigm has been a challenge. In 1992, Australian biologist, Michael Archer wrote, “Indeed, evolutionary scientists are baffled about the ancestry of the platypus.”

As baffling as the platypus was in 1992, it is even more so today, despite the availability of genomic sequencing. Francis S. Collins, past Director of the National Human Genome Research Institute, concedes: “At first glance, the platypus appears as if it was the result of an evolutionary accident. But as weird as this animal looks, its genome sequence is priceless for understanding how mammalian biological processes evolved.”

In a 2008 BBC interview with Helen Briggs, geneticist Mark Batzer, from Louisiana State University notes: “One big surprise was the patchwork nature of the genome with avian, reptilian, and mammalian features.”

What is missing from Collin’s “priceless for understanding” is how the platypus fits into the Tree of Life sequence as Darwin envisioned. No wonder Darwin struggled with the platypus knowing that it contradicting his theory of natural selection—the Platypus should have become extinct. In a 1860 letter to Charles Lyell,  Darwin explains that the

I quite agree with you on the strange and inexplicable fact of Ornithorhynchus having been preserved.

Even in the context of the gene-centric Modern Synthesis theory, genetics seems to play an array of confounding evolution roles. In the butterfly, similar genes are associated with different forms and functions. In the octopus, different genetics results in similar forms and functions. In the platypus, the same genes in different species are associated with the same functions.

Genes are independent, not sequential. As Richard Gibb points out in the Nature journal, it “all points to how idiosyncratic evolution is.”

In Notebook D, Darwin wonders, “when will Ornithorhynchus come in circle?” noting, “Such difficulties will always occur if animals are thought to have been created.” For Darwin, his theory followed an ideology, not the scientific evidence.

After 150 years since the publication of The Origin of Species, the Platypus continues to strike terror in the evolution industry. Jerry Coyne, the consummate neo-Darwinist, in Why Evolution is True never even mentions the Platypus—for good reasons.

According to Alan Love of the University of Minnesota, in Evolution, The Extended Synthesis, published by The MIT Press, “The vigor of these kinds of controversies has led one researcher [Massimo Pigliucci] to ponder whether an extended evolutionary synthesis is just around the corner or simply an impossible chimera.”

Evolution was once a theory in crisis, now evolution is in a crisis without a theory.

References available upon request

Francis Collins, the past director of the Human Genome Project and current director of the National Institute of Health (NIH), and Charles Darwin have pursued a common cause—a belief in evolution supported by deductive reasoning.

Both Collins and Darwin abandoned the inductive Scientific Method reasoning process to embrace deductive reasoning. Their resulting conclusions on “Junk DNA” and “Natural Selection” are similar.

While the DNA regions not known to code for proteins were thought to be only “Junk DNA” by Collins, Darwin thought that Natural Section was the driving force of evolution.

“Junk DNA”, a term that was introduced in 1972 by Susumu Ohno, was a provisional label for the portions of a genome sequence for which no discernible function had been identified.

What evidence drove Collins and Darwin to these conclusions? The answer is what they “thought”—not based on the scientific evidence from nature.

Darwin’s “I think” caption for the “Tree of Life” drawing in 1837, highlights that it was Darwin’s thinking process drove the theory—not evidence from nature. The concept of natural selection was based on Darwin’s belief in evolution supported only by imaginary illustrations. Darwin explains in The Origin of Species–

In order to make it clear how, as I believe, natural selection acts, I must beg permission to give one or two imaginary illustrations.

It does not take a Ph.D. to know that “imaginary illustrations” do not qualify as scientific evidence. Darwin’s “I think” approach to natural selection has eventually lead to the demise of natural selection as the driving force for the origin of species.

No big surprise, then, natural selection ironically became Darwin’s biggest problem. In his own words –

Natural selection… is by far the most serious special difficulty which my theory has encountered.

Italian geneticist Giuseppe Sermonti agrees -

Natural selection could perhaps be invoked as a mechanism accounting for the survival of the species. But the claim that natural selection is creative of life… can only leave one dumbstruck.

Like Darwin, Collins thought that “Junk DNA” was only a remnant of millions of years of evolution. Collins used suspected “Junk DNA” as evidence to support evolution. In his 2006 book entitled The Language of God, Collins tells us that it “strains credulity” to even think that “Junk DNA” could be functional in the cell. Collins explains -

Darwin’s theory predicts that mutations that do not affect function (namely, those located in “junk DNA”) will accumulate steadily over time.

Like Darwin’s dilemma over natural selection, Collins now sees that his thoughts on the evolutionary role of “Junk DNA” are no longer valid. For Collins, “Junk DNA” are now, in Darwin’s words, the “most serious special difficulty which my theory has encountered.”

Collins new book entitled The Language of Life contradicts his original “Junk DNA” thinking –

The discoveries of the past decade, little known to most of the public, have completely overturned much of what used to be taught in high school biology. If you thought the DNA molecule comprised thousands of genes but far more “junk DNA”, think again.

“Junk DNA” is now known not to be junk after all. Collins explains –

These regions are not just filler, however. They contain many of the signals that are needed to instruct a nearby gene about whether it should be on or off at a given developmental time in a given tissue. Furthermore, we are learning that there may be thousands of genes hanging out in these so-called deserts that don’t code for protein at all. They are copied into RNA, but those RNA molecules are never translated — instead, they serve some other important function.

Collins’ toss of “Junk DNA” is analogous to Darwin’s natural selection toss. “Junk DNA” is no longer considered to be evidence for evolution.

According to WIKIPEDIA, the term “Junk DNA” “is currently an outdated concept, being used mainly in popular science and in a colloquial way in scientific publications, and may have slowed research into the biological functions of noncoding DNA.”

The evidence is clear, biological evolution exists only as a myth founded on speculative “I think” evidence—not scientific evidence. The mantra, “science has proven evolution to be true”, continues only as empty deductive rhetoric.

In 1995, Edward B. Lewis, Christiane Nüsslein-Volhard, and Eric F. Wieschaus were awarded the Nobel Prize in Physiology or Medicine for their work on HOX genes. During the 1950’s, geneticist Edward B Lewis discovered the Bithorax complex (BX-C) group of HOX genes in the fruit fly Drosophila melanogaster.

The BX-C HOX gene controls the embryonic development and differentiation of the basic body plan of the fruit fly. HOX is an acronym for homeobox gene, meaning the same or similar gene. The BX-C is now known as a HOX gene—a DNA sequence within genes that is typically about 180 base pairs long.

While Drosophila research was at the forefront of biology and genetics for the first half of the 20th century, not until later in the century following the advent of molecular biology was the role of the HOX gene better comprehended. “It was then that biologists began to come to grips with the incredible homology across species,” said Corey Goodman of the University of California, Berkeley.

Christiane Nüsslein-Volhard, a German, along with Eric F. Wieschaus, an American, emerged as leading HOX gene investigators while focusing on the embryogenesis of the fruit fly Drosophila. HOX genes exist throughout the animal kingdom; at least one HOX cluster exists in Animal Kingdom species.

Excitement at the turn of the century centered on the prospect that Darwin’s “slight, successive” changes might be demonstrated in the evolution of the HOX genes. HOX gene similarity can be stunning. The mouse eye HOX gene is so similar to the Drosophila HOX gene, the mouse and Drosophila HOX genes are interchangeable. The same is true for Hox clusters, HOXA, HOXB, HOXC, and HOXD found in the mouse and humans.

Since HOX genes are now known to act as switches during embryological development, the HOX gene discovery fueled the concept that Darwin’s evolutionary changes originated during embryological development. This concept was compatible with Ernst Haeckel’s “biogenetic law” of “ontology, recapitulates phylogeny” theory that was embraced by Darwin. The popular term is now known as the “evo-devo” theory.

“Developmental biologists have observed a small set of genes [HOX genes],” notes biologist Ramray Bhat, “coordinating organismal development, to be highly conserved across the multicellular kingdom. They call these genes the Development Genetic Toolkit.” In part, surprisingly, the HOX gene demonstrates conservation.

In the quest to validate the evo-devo theory, the central issue centers on the evidence for “slight, successive” evolutionary changes in the HOX genes. After four decades of research, however, the evidence continues to be even more evasive since the evidence favors HOX gene conservation, not Darwin’s “slight, successive” evolutionary changes.

According to Harvard evolutionary biologist, Richard Lewontin in an interview with Susan Mazur during 2008, “there’s no question that the development of an egg is not dependent solely on the genes [HOX genes] and nucleus, but on the structure of the eggs as laid down to some extent.” Development is influenced by epigenetic factors: factors beyond genetics and HOX genes.

The once widely popular evolutionary status of HOX genes has now slid into silence, along with once popular evo-devo hype. Since 2009, in the journal Molecular Biology and Evolution published by Oxford Journals, the vanguard of molecular evolutionary biology, only six papers have been published on HOX gene research (see below).

At stake is whether the evidence from the HOX genes actually supports Darwin’s elusive “Tree of Life” theory. Amazingly, the recent discovery of large differences in HOX genes between closely related species by John F. Mulley and Peter W. H. Holland of Oxford University actually undermines Bhat vision of evolutionary conservation role in the HOX gene.

Richard Dickerson, director of molecular biology at the University of Minnesota points out that “the more one approaches the molecular level in the study of living things, the more similar they appear, and the less important the differences.”

Hox genes are like Perili tires. Even though the Focus and Ferrari can sport the same Pirelli tires, does not mean the cars were produced in the same factory—the Focus is not the ancestor of a Ferrari. The Focus and the Ferrari, while similar, are independent entities.

“Theories are cheap,” Richard Lewontin pines, “and people make a living by making theories.” In the words of Swedish cytogeneticist, Antonio Lima-de-Faria, “evolution is the opium of biologists.” Withdrawal is inevitable.

Within the evolution industry, the HOX genes are the latest “facts of evolution” to slid into silence.

Molecular Biology and Evolution papers published by Oxford Journals, 2009 – 2011

Jenny Widmark, Görel Sundström, Daniel Ocampo Daza, and Dan Larhammar. Differential Evolution of Voltage-Gated Sodium Channels in Tetrapods and Teleost Fishes. Mol Biol Evol (2011) 28(1): 859-871

Laura C. Ferguson, Jack Green, Alison Surridge, and Chris D. Jiggins. Evolution of the Insect Yellow Gene Family. Mol Biol Evol (2011) 28(1): 257-272

Silvan Oulion, Mélanie Debiais-Thibaud, Yves d’Aubenton-Carafa, Claude Thermes, Corinne Da Silva, Sylvie Bernard-Samain, Frédéric Gavory, Patrick Wincker, Sylvie Mazan, and Didier Casane. Evolution of Hox Gene Clusters in Gnathostomes: Insights from a Survey of a Shark (Scyliorhinus canicula) Transcriptome. Mol Biol Evol (2010) 27(12): 2829-2838

John F. Mulley and Peter W. H. Holland. Parallel Retention of Pdx2 Genes in Cartilaginous Fish and Coelacanths. Mol Biol Evol (2010) 27(10): 2386-2391

Peter W. Osborne and David E.K. Ferrier. Chordate Hox and ParaHox Gene Clusters Differ Dramatically in Their Repetitive Element Content. Mol Biol Evol (2010) 27(2): 217-220

Shigehiro Kuraku, Axel Meyer, and Shigeru Kuratani. Timing of Genome Duplications Relative to the Origin of the Vertebrates: Did Cyclostomes Diverge before or after? Mol Biol Evol (2009) 26(1): 47-59

In The Origin of Species, Charles Darwin envisioned that “natural selection acts solely by accumulating slight, successive, favourable variations; it can produce no great or sudden modifications.”

Since 1859, the search for Darwin’s “slight, successive” accumulated actions of natural selection has become a driving scientific and societal phenomenon. In 1872, the British Parliament commissioned the HMS Challenger for first international exploration to discover the “missing links” resulting from natural selection.

Like the HMS Challenger experience, evidence for “slight, successive” evolutionary changes continues to be an elusive pursuit—in the fossil record and now in molecular biology. Darwin’s dilemma deepens with the latest evidence from the Denisova caves in Russia.

In 2008, Russian archeologists working at the site of Denisova Cave in the Altai Mountains of Siberia uncovered a small bone fragment from the fifth finger of a juvenile hominin, initially dubbed as the “X-woman”. A tooth had been previously unearthed in the same cave area.

Interest in the project began to develop momentum. In March of this year, Kate Wong in Scientific America published an article entitled “No Bones about It: Ancient DNA from Siberia Hints at Previously Unknown Human Relative”—hinting at an ancestral evolutionary relationship to humans. Early this year, expectations were running high that the pinky and tooth was eventually going to demonstrate a human evolution link simply by DNA analysis.

To demonstrate the molecular “slight, successive” link to humans, a team of scientists led by David Reich, Richard Green, Johannes Krause along with Swedish biologist Svante Pääbo from the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany sequenced mitochondrial DNA (mtDNA) extracted from the fragment.

The investigators were startled by the findings. Contrary to initial expectations, the report published in the December 23 issue of the journal Nature found that fossilized finger “was not involved in the putative gene flow from Neanderthals into Eurasians” and that the tooth was “distinct from Neanderthals and modern humans”.

“We thought it was a mistake when we first saw it,” Reich wrote. “But it’s real.”

Richard Green of the University of California, Santa Cruz noted: “The story [human evolution] now gets a bit more complicated.”

Evidence from the Denisova finger mtDNA, rather than pointing to “slight, successive” changes in human evolution, highlights a deeper evolutionary dilemma—there are no known “slight, successive” molecular changes accounting for human evolution.

At a news conference, Krause said that the lab, sequencing mtDNA from several samples, was startled to discover the unexpected. “The sequence was similar to humans, but very distinct from humans,” he said. After performing many tests to ensure the results were not an artifact, “I called Svante on his mobile [phone] and told him to sit down.”

Pääbo, who was in the U.S. at the time, said, “It was absolutely amazing. At first, I didn’t believe him. I thought he was pulling my leg…. This was some new creature that has not been on our radar screens so far.”

Professor Chris Stringer, human origins researcher at London‘s Natural History Museum and one of the leading proponents of the recent single-origin hypothesis, remarked: “This new DNA work provides an entirely new way of looking at the still poorly understood evolution of humans in central and eastern Asia.”

Twenty-eight coauthors worked on the paper, including researchers from Germany, Spain, China, Russia, Canada, and the United States. This research was supported by the Max Planck Society, the Krekeler Foundation, the U.S. National Institutes of Health, and the U.S. National Science Foundation.

This highly financed international evolution industry initiative, following in the legend of the HMS Challenger, once again only found new species—not “missing links”. The fossil, now known as Denisova hominin, is “very distinct from humans” and certainly not one of the “slight, successive” human ancestors as envisioned by Darwin.

Evolution once a theory in crisis, is now in crisis without a theory.

Critical of The Origin of Species, Charles Darwin in a letter to Hugh Falconer in October 1862, Darwin wrote, “I look at it as absolutely certain that very much in the Origin will be proved to be rubbish; but I expect and hope that the framework will stand.” 

Darwin’s conceptual framework of “slight, successive” changes over time had remained intact for 150 years, until the evidence from the human genome project delivered the decisive destruction of the original “framework”.   

J. Craig Venter, the microbiologist turned entrepreneur that mapped the human genome and re-produced what he calls “the first synthetic species”, concluded during a 60-Minute CBS interview with Steve Kroft on Sunday, November 21 that the human genome project has been a “bust”.

In the aired TV segment entitled “J. Craig Venter: Designing Life”, CBS touted that Venter’s new synthetic species “gets its genetic instructions from a synthetic chromosome made by man, not nature”. What the CBS investigative report failed to perceive through the California coastal fog was that the “new synthetic species” was just a copy from nature, not man.  

According to molecular biologist Jim Collins of Boston University writing in the journal Nature, “Its [Venter’s] genome is a stitched-together copy of the DNA of an organism that exists in nature, with a few small tweaks thrown in.”

Mark Bedauv of Reed College in Portland, Oregon, also writing in the Nature commentary called Venter’s new species “a normal bacterium with a prosthetic genome.”

Molecular geneticist Georgia Purdom noted that Venter’s kind of genetic engineering is “like taking the hard drive of computer #1 and putting it into computer #2 that has had its own hard drive removed. So effectively computer #2 becomes computer #1.” Even Venter, when questioned directly, agrees, we “didn’t create life from scratch.”

Aside from the foggy CBS misrepresentation of the “new synthetic species”, more to the point, in the un-aired 60-Minute segment and posted as a trailer entitled “Extra: The Human Genome & Disappointment”, Venter explains to Kroft in the following interview why “he is disappointed not many research breakthroughs have happened since the human genome was mapped nearly ten years ago” -

Steve Kroft: You have mentioned the human genome and all the things it was supposed to do. Actually, a lot of people have been disappointed.

J. Craig Venter: They should be.

Steve Kroft: Because great things were promised and it hasn’t really happened.

J. Craig Venter: Ya

Steve Kroft: Yet?

J. Craig Venter: Well, it is early when you think of new drugs coming out. The cycle of a drug is 15 years from early discovery to getting one out on the market. We are only 10 years into the human genome. But it was definitely over sold in part to get the billions of dollars from congress for the program. I mean there were scientists saying within a decade all human diseases would be cured. Now that we are a decade out, not too many of them have been done.

Steve Kroft: You said that it was over-sold and there was a lot of hype. Some would say you were part of that.

J. Craig Venter: I’ve been optimistic about the future, about what it will do. I remain optimistic, but I have never said that it would cure diseases. I thought we would get to preventive medicine. Actually, I have thought we would get there faster than we have. I’ve been actually amazed at the lack of human genome research in this past decade.

Steve Kroft: Why has it been a bust?

J. Craig Venter: Well, there wasn’t a lot of funding for it. The funding all switched to zoo biology. NIH [National Institute of Health] sequenced all kinds of animals -all kinds of mammals, lizards, alligators, and horses. Thinking that if we have all these other genomes they would tell us how to interpret our own genome. Turns out it was not all that useful once you get past the mouse, all mammals share pretty much the same set of genes.

The human genome project has been an evolutionary “bust”. The NIH was looking to sequence the simpler “slight, successive” changes in animal genomes so that they “would tell us how to interpret our own genomes”. Stunningly, Venter points out that the “slight, successive” genetic differences between species do not exist—in fact, “all mammals share pretty much the same set of genes”.

Without question, the evidence in genetics to support Darwin’s framework of “slight, successive” changes from the simple to the more complex simply does not exist.

As Australian molecular biologist, Michael Denton explains – “At a molecular level there is no trace of the evolutionary transition from fish to amphibian to reptile to mammal.”

Richard Dickerson, director of molecular biology at the UCLA points out – “The more one approaches the molecular level in the study of living things, the more similar they appear, and the less important the differences.”                     

Evidence, even stemming from the human genome project, has been a “bust” for evolution. The scientific evidence clearly undermines and contradicts the neo-Darwinian paradigm of evolution—gradual genetic changes through mutation and natural selection. Darwin’s framework of evolution through “slight, successive” changes has been irreparably destroyed.

No wonder the evolution industry is desperately searching for epigenetic factors—factors other than genetics. Evolution was once a theory in crisis, now evolution is in crisis without a theory. As leading Italian geneticist Giuseppe Sermonti notes, “Science has taken on the wager… and lost.”

In his autobiography, Charles Darwin notes, “Towards the end of the work I gave my well abused hypothesis of Pangenesis. An unverified hypothesis is of little or no value”—the First-Wave of evolutionary thought. Today, Darwin’s sentiments on pangenesis have re-emerged, however, this time on genetics.

In this week’s edition of the journal Science published by the American Association for the Advancement of Science (AAAS), the focus is on epigenetics. An on-line issue even features a video by Science editor Guy Riddihough asking a number of top researchers a simple question: “What’s your definition of epigenetics?” And, “Their answers aren’t quite so simple,” according to Riddihough.

While Darwin’s theory of pangenesis in The Origin of Species gained little support, the emerging gene-centric model Second-Wave for evolution proposed by the giants of evolution starting with Theodosius Dobzhansky, Julian Huxley, Ernst Mayr, and Francis Crick, became the foundation of evolution of theory over the during the late twentieth century.

Crick named the theory, the “Central Dogma” of evolution. Evolutionary theory was envisioned as simply a process of genetic mutations acted on by natural selection.

Since then, the stage has been set to discover the anticipated Darwinian “slight, successive” sequence of genetic mutations associated with the evolution of new species. Not until just the last ten years has last the technological frontier been conquered, DNA sequencing, to validate the gene-centric theory of evolution.

Now with genetic evidence available to valid the Second-Wave, scientists are abandoning the gene-centric evolutionary theory for one big reason; there are no “slight, successive” genetic changes to validate the gene-centric theory of evolution as anticipated by neo-Darwinism, the Modern Synthesis, or the Modern Evolutionary Synthesis. From nature, the evidence is clear; any mechanism for evolution must exist beyond genetics—epigenetic.

Epigenetics major problem is, as Riddihough highlights, there is no consensus on what constitutes epigenetics, “Although epigenetics generally refers to the inheritance of variation above and beyond changes in DNA sequence, the term is becoming shorthand for a variety regulatory systems involving DNA methylation, histone modification, nucleosome location, or noncoding RNA.”

The once simple Second-Wave theory of mutations acted on by natural selection has now been given way to a Third-Wave of yet a vastly more complex theory, in yet some unknown system, and with yet some unknown mechanisms, as Riddihough highlights.

The Third-Wave of genetics, including epigenetics, has completely replaced the Second-Wave realm of theoretical evolution. Massimo Pigliucci in his new book entitled Evolution-The Extended Synthesis published by MIT Press, recognizes that the fundamental tenets of Modern Synthesis “are being challenged as either inaccurate or incomplete” and “all these molecular processes clearly demolish the alleged central dogma.”

To address the Second-Wave crisis and pave the way to the Third-Wave, Pigliucci and Gerd Muller in the summer of 2008 convened a workshop at the Konrad Lorenz Institute for Evolution and Cognition Research in Altenberg near Vienna, Austria. 

The workshop was entitled “Toward an Extended Evolutionary Synthesis?” Evolutionary academians from sixteen universities participated in the workshop. The workshop became known as the “Altenberg-16” and dubbed “The Woodstock of Evolution.”

Today, evolution is a philosophy looking for the evidence to support the theory. As such, the evolutionary industry has completed abandoned the Scientific Method.

Nature has spoken. Evolution, once a theory in crisis, is now in crisis without a theory.

Jerry Coyne, in his new book entitled Why Evolution is True, conveniently circumvents any reference to the butterfly, as does Darwin-Discovering the Tree of Life by Niles Eldridge. The California State sponsored website, “Understanding Evolution,” website completely ignores the notorious nature of butterflies—metamorphosis.

So, why is the evolution industry silent on butterfly metamorphosis? The answer is simple—the same DNA is found in all four life cycles; egg, caterpillar (larva), cocoon (pupa) and butterfly (adult). Metamorphosis, to the theory of evolution, is an enigma.

For over 3,500 years, to the Egyptians, Chinese, and Greeks, the butterfly symbolism was derived from the unique butterfly life cycles. The egg first develops into the caterpillar before transitioning into the cocoon. Amazingly, inside the cocoon, the caterpillar is destroyed before developing into the stunningly colorful butterfly cycle.

According to the theory of evolution, the DNA (genotype) determines the form (phenotype). The fact that the metamorphosis of the butterfly uses the same DNA in all four cycles, contradicts gene-centric theories of evolution.

With the same DNA producing different forms, the message is clear: DNA is not the blueprint controller of life. Genetic evidence from the butterfly undermines the Central Dogma of evolution—“one gene, one protein.”

The butterfly is not an isolated phenomenon. Italian geneticist Giuesppe Sermonti points out that “examples of highly divergent forms possessing one and the same DNA are so conspicuous and so numerous that the marvel is that they have attracted so little attention.”

Even more astounding in the case of the butterfly, Sermonti notes, “what we call metamorphosis is not really a change in form. Once the pupa, or chrysalis, stage is reached, the caterpillar starts emptying itself: its organs dissolve, and its outer covering is shed. Only certain groups of cells, called marginal disks, remain vital. From these cells develop all the structures of adult.”

The larva of the butterfly not only changes form, but actually dissolves before rebuilding into the structure of a butterfly—a new life-form. From the same DNA arises a completely different organism. According to Sermonti, the same DNA, then, can play different roles: “DNA may lend itself to such diverse forms, but it is not the DNA that imposes the blueprint.”

The presence of the same DNA in different life-forms has been given the term “genomic equivalence”. This means that control of the cell is beyond the DNA, or “epigenetic.”

Brian Goodman, Canadian developmental biologist and key founder of theoretical biology, focuses on the methods of mathematics and physics to understand processes in biology concludes –

While genes are responsible for determining which molecules an organism can produce, the molecular composition of organisms does not, in general, determine their form.

H. Frederik Nijhout of the Department of Biology at Duke University, a critic of Crick’s central dogma, came to the conclusion that “the only strictly correct view of the function of genes [DNA] is that they supply cells, and ultimately organisms, with chemical materials.”

The butterfly nightmare phenomena in evolution adherents are real, the result of the holding on to the belief: DNA mutation + natural selection = evolution—a theory not supported by evidence in nature.

State funded evolutionary education along with the high priests of evolution, Jerry Coyne, and Niles Eldridge, should now deliver a therapeutic service to humanity by addressing blatant contradictions between the theory of evolution and natural history.

No wonder French geneticist, discoverer of the Down syndrome, Jérôme Lejeune, cut to the chase – “There is no theory of evolution.”

This year, 2010, has not been a good year for the “out of Africa” evolutionary theory of human origins. The following is why.

In October 2009, Time Magazine recognized Ardipithecus ramidus, now known as “Ardi,” the number one of “Top 10 Scientific Discoveries” of 2009. The journal Science declared Ardi the “breakthrough of the year.”

Ardi, an nearly complete fossilized female skeleton, was discovered by Timothy Douglas White, an American Paleoanthropologist and Professor of Integrative Biology at the University of California, Berkeley in the arid badlands near the Awash River in Ethiopia in 1994.

Examination and description of Ardi took nearly 15 years before releasing publication. Although it is not known whether Ardi’s offspring actually developed into Homo sapiens, the discovery was expected to be of great significance since Ardi is the oldest known hominid fossil. Ardi had been theorized to be an ancestor to Australopithecus afarensis, more commonly known as Lucy.

John Noble Wilford, science writer for the New York Times reported that David Pilbeam, a professor of human evolution at Harvard University said that the Ardi skeleton represents “a genus plausibly ancestral to Australopithecus [Lucy]” and began ‘to fill in the temporal and structural ‘space’ between the apelike common ancestor and Australopithecus.”

In the excitement, the Discovery Channel produced a series of articles and videos arguing how Ardi, not the chimpanzee, were the common ancestors to humans. The American Association for the Advancement of Science, publisher of the journal Science, developed an educational series in five separate publications on Ardi.

Since Ardi was discovered in east Africa, the finding gained further support for the popular “out of Africa” model first proposed by Charles Darwin. In The Descent of Man, Darwin hypothesized - 

In each great region of the world the living mammals are closely related to the extinct species of the same region. It is, therefore, probable that Africa was formerly inhabited by extinct apes closely allied to the gorilla and chimpanzee; and as these two species are now man’s nearest allies, it is somewhat more probable that our early progenitors lived on the African continent than elsewhere

Almost fifty years after the publication of The Descent of Man, Darwin’s speculations seemed to be supported following the discovery of numerous hominid fossils in several areas of Africa. The “out of Africa” model continued to be the most widely recognized theory since the publication of the Descent of Man—until May 2010.

Svante Pääbo of the Department of Evolutionary Genetics at the Max-Planck Institute for Evolutionary Anthropology in Germany published in the journal Science in May 7, 2010, an article on the sequencing of the genome of the Neanderthal man entitled “A Draft Sequence of the Neanderthal Genome”.

According to Gregory Hannon of Cold Spring Harbor Laboratory in Laurel Hollow, N.Y., Svante Pääbo’s “publication of the full Neanderthal genome is a watershed event, a major historical achievement.” Pääbo noted, “In some of us they live on, a little bit” with on major caveat – not in African descendants.

Mark Henderson, science writer for The Sunday Times, London, explains – “Human genomes from France, China, and Papua New Guinea showed Neanderthal signatures, but not those from West and Southern Africa.” The absence of Neanderthal genetic evidence in Africans has devastated Darwin’s treasured “out of Africa” theory pushing the relevance of Ardi as an ancestor to humans into extinction.

Genetics is not Ardi’s only problem with the “out of Africa” theory—so is the paleontological analysis. Time Magazine, and the journals Nature and Science, after more thoroughly examining the available data, has started slow process of recanting on the role of Ardi as an early ancestor to man.

In the Time article entitled “Ardi: The Human Ancestor Who Wasn’t” now highlight that “Two new articles being published in Science question some of the major conclusions of Ardi’s researchers, including whether this small, strange-looking creature is even a human ancestor at all.”  

The British science journal Nature reports: “Ardi may be more of an ape than human.” In the article, Esteban Sarmiento, a primatologist at the Human Evolution Foundation argues in the article Comment on the Paleobiology and Classification of Ardipithecus ramidus, that the Ardi could not be an evolutionary ancestor to humans:

[White] showed no evidence that Ardi is on the human lineage…. Those characteristics that he posited as relating exclusively to humans also exist in ape and ape fossils that we consider not to be in the human lineage.

With Ardi as the celebutante, the evolution industry, in desperation to connect the dots for a human evolution theory, has once again fallen into another humiliating about-face based on the inescapable scientific evidence.

As the “out of Africa” model undergoes extinction, scientists are beginning to investigate the “multiregional origin of humans” theory in which man is simply “a single, continuous human species”—a theory approaching the recorded biblical account for the origin of man.

The fruit fly is celebrating 100 years of research. Charles W. Woodworth at the University of California, Berkley, at the turn of the twentieth century, was the first to use the fruit fly as model in the study of genetics. Today, Drosophila melanogaster, the common fruit fly, has become one of the most studied organisms in biological research, particularly in the field of genetics.

In 1910 following Woodworth’s footsteps, at Columbia University from the top floor of Schermerhorn Hall, now known as the Fly Room, Thomas Hunt Morgan confirmed and extended Gregor Mendel’s basic principles of genetics. A year later, Morgan published his findings in Science, establishing the foundation for the emerging neo-Darwinism movement.

Morgan, in the book entitled The Mechanism of Mendelian Inheritance (1915) demonstrated how mutations using radiation on two-winged fruit flies resulted in four-winged fruit flies. The four-winged fruit fly was widely heralded as the earliest evidence that the first evolutionary step to produce a new species was a mutation.

The question, however, centered on whether the mutated four-winged fruit fly was a new species or an unsustainable aberrational freek. By 1963 after decades of research, the question could be answered definitively. Ernst Mayr, Charles Darwin’s twentieth century Bulldog, viewed the mutated four-winged fruit flies as “such evident freaks that these monsters can be designated only as ‘hopeless.’ They are so utterly unbalanced that they would not have the slightest chance of escaping elimination.” Mutation is not the gateway to evolution.

While mutations on the two-winged fruit fly served as a window to study theroretical evolutionary genetics for decades, mutations are now known not supply the raw materials for evolution. Italian geneticist Giueseppe Sermonti explains –

One spur to research on mutations was the hope that an accumulation of these might lead to a new species. But this never happened.

The fruit fly as a model for evolution via mutations gets even worse—there are no “slight, successive” genetic changes even between over 1,400 closely related Drosophila species.

The number of nucleotide base pairs Drosophila species ranges from 127 to 800 million. The probability of constructing a Tree of Life with “slight, successive” changes in nucleotide base pairs from species to species approaches the realm of impossible.

Each species of Drosophila appears to remain distinct and unique. The following table is the number of estimated genome sizes as measured by the number of nucleotide base pairs in several different Drosophila genomes.

Pierre-Paul Grassé, past-president of the French Academie des Sciences in the book entitked  Evolution of Living Organisms concludes – “The fruit fly [Drosophila melanogaster],the favorite pet insect of the geneticists, whose geographical, biotopical, urban, and rural genotypes are now known inside out, seems not to have changed since the remotest times”—evolution never happened. 

No wonder genetic researchers at Bioinformatics Research Center, North Carolina State University now bring into question whether genes even play a role in evolution between related Drosophila species. Wen-Ping Hsieh and collegues published in Genetics -

An emerging issue in evolutionary genetics is whether it is possible to use gene expression profiling to identify genes that are associated with morphological, physiological, or behavioral divergence between species and whether these genes have undergone positive selection. (1)

Genetic researchers from the Department of Ecology and Evolutionary Biology, University of Arizona, similarly discovered that “no strong evidence” in gene selection exists between Drosophila species and the respective proteins produced, “divergent expression”. Between Drosophila species, changes in genes do not correllate with changes in proteins. Jeffrey M. Good and collegues in an article published in Molecular Biology and Evolution, 2006, conclude -

Overall, we found no strong evidence for an increase in the incidence of positive selection on protein-coding regions in genes with divergent expression in Drosophila (2)

Genomic research looking for the “slight, successive” genetic changes required by neo-Darwinism is no friend of evolution. The survivors of 100 years of lab torture continue just as fruit flies.

The genome of D. melanogaster was sequenced in 2000. Most surprisingly, nearly 75% of known human disease genes are now known to have a recognizable match in the genetic code of fruit flies, and 50% of fly protein sequences have mammalian homologs. Mutations are either neutral or lead to disease—not evolution.

Today, over 100 years later, Drosophila serves as a genetic model for several human diseases including the neurodegenerative disorders Parkinson’s, Huntington’s, spinocerebellar ataxia and Alzheimer’s disease.

Reflecting on the limits of genetics in establishing the validity of evolution, Italian geneticist Giuseppe Sermonti weighs in –

Science has taken on the great wager … and lost.

1.  Wen-Ping Hsieh, Tzu-Ming Chu, Russell D. Wolfinger, and Greg Gibson. Mixed-Model Reanalysis of Primate Data Suggests Tissue and Species Biases in Oligonucleotide-Based Gene Expression Profiles. Genetics. 2003. 165: 747-757

2.  Jeffrey M. Good, Celine A. Hayden, and Travis J. Wheeler. Adaptive Protein Evolution and Regulatory Divergence in Drosophila. Molecular Biology and Evolution. 2006, 23(6):1101-1103

Genetic evidence now points to one ugly fact for the theory or evolution; Autism and Alzheimer’s disease are the result of genetic mutations.

ScienceDaily on May 3 reported that investigators at the Pediatric Academic Societies (PAS) annual meeting in Vancouver, British Columbia, that new research has uncovered two additional genes involved with autism.

An estimated one in 110 U.S. children has autism, which negatively affects behavior, social skills, and communication.

The risk for the disorder can be now be considered an inherited genetic disease, based on a study performed by professors Daniel Notterman at Penn State, and Ning Lei at Princeton University.

Lei and colleagues analyzed data from the Autism Genetic Resource Exchange (AGRE) on 943 families, most of whom had more than one child diagnosed with autism and had undergone genetic testing. Investigators compared the prevalence of 25 gene mutations in the AGRE families with a control group of 6,317 individuals without developmental or neuropsychiatric illness.

Mutations in four genes within the AGRE families were identified. Two of the genes previously were shown to be associated with autism and often are involved in forming or maintaining neural synapses — the point of connection between individual neurons.

One of the new genes identified was neural cell adhesion molecule 2 (NCAM2). NCAM2 is expressed in the hippocampus of the human brain — a region previously associated with autism.

“While mutations in the NCAM2 gene were found in a small percentage of the children that we studied, it is fascinating that this finding continues a consistent story — that many of the genes associated with autism are involved with formation or function of the neural synapse,” Dr. Lei said. “Studies such as this provide evidence that autism is a genetically based disease that affects neural connectivity.”

According to Jerry Coyne in his widely acclaimed book entitled Why Evolution is True, evolution originates from mutations. Coyne explains,

The first is the idea of evolution itself. This simply means that a species undergoes genetic change over time. That is, over many generations a species can evolve into something quite different, and those differences are based on changes in DNA, which originate as mutations.

With Autism, however, the genetic change is certainly not beneficial. The same is true for the newly discovered genetic mutation associated with Alzheimer’s disease.

 In the June 10 online issue of the journal Cell, researchers from New York Universty’s Center of Excellence on Brain Aging and the Silberstein Alzheimer’s Institute, reported their findings that a mutation of a gene associated with early onset Alzheimer’s blocks a key recycling process necessary for brain cell survival.

The gene, presenilin 1 (PS1), performs a crucial house-cleaning service by helping brain cells digest unwanted, damaged and potentially toxic proteins. Once mutated, however, the gene fails to recycle and eliminate the potential toxins from causing cellular damage to brain cells resulting in Alzheimer’s disease.

“We believe we have identified the principal mechanism by which mutations of PS1 cause the most common genetic form of Alzheimer’s disease,” said study co-author Ralph A. Nixon, professor in the departments of psychiatry and cell biology as well as director at New York University.

Scientific evidence from Autism to Alzheimer’s disease, rather than supporting evolution as campaigned evolution militants like Jerry Coyne and Richard Dawkins, contradicts the theory of evolution.

Evolution is a theory in crisis. No small wonder, even ardent atheists Fodor and Piattelli-Palmarini were compelled to write “Why Evolution is Not True” (2010).  

I cannot swallow Man [being that] distinct from a Chimpanzee.

Charles Darwin writes in his Autobiography,

My Descent of Man was published in Feb. 1871. As soon as I had become, in the year 1837 or 1838, convinced that species were mutable products, I could not avoid the belief that man must come under the same law

The chimp, since the nineteenth century, has been the poster-child missing link to humans. In twenty-first century terms, the mammalian Y chromosomes were expected to be similar, as speculated by Darwin. However, new evidence demonstrates Darwin’s speculation to be wrong—the chimp Y chromosome differs radically from humans.

The British journal Nature published a paper in January 2010 titled, “Chimpanzee and Human Y Chromosomes are Remarkably Divergent in Structure and Gene Content,” found that Y chromosomes in the chimp and humans “differ radically in sequence structure and gene content”. In fact,

More than 30% of the chimp Y chromosome lacks an alignable counterpart on the human Y chromosome

Jennifer F. Hughes led the research team at the Whitehead Institute for Biomedical Research, one of the world’s leading centers for genomic research, is located in Cambridge, Massachusetts. The research team concluded –

By comparing the MSYs of the two species we show that they differ radically in sequence structure and gene content

“By conducting the first comprehensive interspecies comparison of Y chromosomes,” ScienceDaily noted, “Whitehead Institute researchers have found considerable differences in the genetic sequences of the human and chimpanzee Ys… The results overturned the expectation that the chimp and human Y chromosomes would be highly similar. Instead, they differ remarkably in their structure and gene content.”

The original chimp genome sequencing completed in 2005 largely excluded the Y chromosome because its hundreds of repetitive sections had typically confound standard sequencing techniques. The chimp Y chromosome is only the second Y chromosome to be comprehensively sequenced.

 Wes Warren, Assistant Director of the Washington University Genome Center, noted

These findings demonstrate that our knowledge of the Y chromosome is still advancing.

Earlier comparative studies between the chimp and human genome had centered on DNA regions that only result in the production of proteins. In addition, not only is the chimp DNA 12% larger than human DNA, the Chimp has 23 chromosomes while humans have only 22 (excluding sex chromosomes in both species).

While the researchers advance the concept that “divergence” from the Chimp occurred 6 million years ago, the more logical explanation is that the chimp is simply a distinct species.

The research was funded by the National Institutes of Health (NIH) and the Howard Hughes Medical Institute (HHMI)

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?

Charles Darwin used the term species more than any other term in The Origin of Species— 1,926 times. Defining the term species, however, has been a problem. Darwin wrote, there “is no possible test but individual opinion to determine which of them shall be considered as species”.

Naturalist Henry Alleyne Nicholson explains, “No term is more difficult to define than ‘species,’ and on no point are zoologists more divided than as to what should be understood by this word.”

Geneticist Laura M. Zahn in looking for the genetic distinction between species, published there results in paper entitled “Background Matters” in the October 2009 edition of Evolution and abstracted in Science. Much to their surprise, Zahn and colleagues discovered that no single genetic allele is known to exist that can define the difference between species.

After 150 years, Darwin’s statement continues to be dead on, “It is all-important to remember that naturalists have no golden rule by which to distinguish species.”

Ironically, a book on the origins of an indefinable term, then and now, ascended into a historical phenomenon.