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.”

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

Ignorance more frequently begets confidence than does knowledge.  Charles Darwin

Darwin argued in The Origin of Species that evolution develops through the processes of natural laws, changing the simple into the complex, in ways analogous to the laws of gravity -

[W]hilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved.

The chromosome is the organizational structure of DNA and proteins in cells. DNA contains the nucleotide sequences that form the genes. During the twentieth century, determining the number of chromosomes in species has been in the investigative forefront.

Since Darwin envisioned that “natural selection acts solely by accumulating slight, successive, favourable variations; it can produce no great or sudden modifications”, according to the theory, chromosomes were expected to demonstrate evolution from the simple into the more complex via “slight, successive” changes.  

While the simplest known organism, Mycoplasma hominis, does have only one chromosome, Darwin’s simple to complex theory quickly breaks down. Unless the Gorilla, Chimpanzee, Cow, Guinea Pig, and Goldfish evolved from Humans, the simple to complex theory of evolution is simply incompatible with the scientific evidence.

If natural selection acts only, as Darwin suggests, by “slight, successive” changes and “must advance by the short and sure, through slow steps”, then scientific evidence from chromosomes clearly contradicts the Darwinian theory of evolution.

In the book Why Evolution is True, Jerry Coyne conveniently and completely overlooks the lack of evidence for “slight, successive” changes in chromosomes. Coyne never even listed the term “chromosome” the Index. Reason—chromosomal evidence destroys the theory of evolution.

Niles Eldridge of the American Museum of Natural History in his companion book Darwin – Discovering the Tree of Life for the Darwin exhibit never mentions that the “slight, successive” sequences of the chromosome never happened. Evolutionist avoid chromosome like the plague. Reason, again—chromosomal evidence destroys the theory of evolution.

The evolution of the chromosome parallels horse evolution tales. Swedish geneticist Heribert Nilsson pointed out as early as 1954 that the “family tree of the horse is beautiful and continuous only in the textbooks.”

In 1996, Stephen J. Gould used stronger words in his book Full House: The Spread of Excellence From Plato To Darwin, concluding that the “popularly told example of horse evolution, suggesting a gradual sequence of changes… has long been known to be wrong.” Rather than “slight, successive” changes as envisioned by Darwin, “fossils of each intermediate species appear fully distinct, persist unchanged, and then become extinct. Transitional forms are unknown.”

Bemoaning the continued use of what he termed “misinformation,” such as horse evolution, Gould, in 2000, pined in a 2000 article that appeared in the journal Natural History – “Once ensconced in textbooks, misinformation becomes cocooned and effectively permanent, because … textbooks copy from previous texts.”

In the molecular world, biochemist Richard E. Dickerson at Cambridge University notes 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 between, for instance, a clam and horse become.”

Molecular biologist Michael Denton clarifies – “Instead of revealing a multitude of transitional forms through which the evolution of the cell might have occurred, molecular biology has served only to emphasize the enormity of the gaps.”

Mounting scientific evidence continues to erode any known comprehensive theory of evolution. The evolution industry should heed Darwin’s warning that “[i]gnorance more frequently begets confidence than does knowledge” by starting to count chromosomes.

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 

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.

While researchers in Germany, announced completion of the first draft of the Neanderthal genome, to coincide with the 200th anniversary of Charles Darwin’s birth, the hoped for links to human evolution are still missing.

 The genome team led by geneticist Svante Paabo after isolating 3.7 billion base pairs could only conclude:  ”We’re currently analyzing if we see evidence in the Neanderthal genome of contribution from human ancestors,” Paabo said. “That question I think is still totally open.”

Again, this big golden nugget of evolution, like the fossil record, continues as the emperor without clothes. In the Guardian, palaeontologist Simon Conway Morris writes:

 “[P]erhaps now is the time to rejoice not in what Darwin got right, and in demonstrating the reality of evolution… “Isn’t it curious how evolution is regarded by some as a total, universe-embracing explanation, although those who treat it as a religion might protest and sometimes not gently. Don’t worry, the science of evolution is certainly incomplete.”

Even the New York Times writer, Carl Safina, in an essay for the science section entitled “Darwinism Must Die So That Evolution May Live” concludes, “So let us now kill Darwin.”

 After 150 years, since the natural mechanism of evolution that Darwin was looking for is still missing, in this post-modern evolution era the birthday party fizzled.