Posts Tagged ‘DNA’

In The Origin of Species, Charles Darwin developed his revolutionary theory of “slight, successive” evolutionary changes. During the mid-nineteenth century, however, knowledge about genes and genetics was speculative at best, no less the evolution of genes.

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.

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In The Origin of Species, Charles Darwin agonized over the gaps in the fossil record. “Why then is not every geological formation and every stratum full of such intermediate links? Geology assuredly does not reveal any such finely graduated organic chain; and this, perhaps,” Darwin pined, “is the most obvious and serious objection which can be urged against my theory.”

To address and justify the “serious objection,” Darwin reasoned that “only a small portion of the surface of the Earth has been geologically explored.” However, in the wake of 150 years of unprecedented paleontological research since the publication of The Origin of Species in 1859, the gaps are even more glaring. Continue Reading

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. Continue Reading

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. Continue reading more

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.

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Faced with the failure of the Stanley-Urey model to explain the origin of life, evolutionary scientists have been exploring the RNA World theory. With only the four nucleic acids required to form RNA rather than the twenty amino acids to form a protein, the chance probability tipped the advantage to the RNA-first theory, but that is not all.

In The Ancestor’s Tale: A Pilgrimage to the Dawn of Evolution, Richard Dawkins explains

“This is the RNA World. To see how plausible it is, we need to look at why proteins are good at being enzymes but bad at being replicators; at why DNA is good at replicating but bad at being an enzyme; and finally why RNA might just be good enough at both roles to break out of the Catch-22.”

The RNA World theory solved the chicken-or-the-egg Catch-22 conundrum. At least that was the hope. Notice Dawkins use of the word “plausible.” Building proteins requires information from DNA, but information in DNA cannot be processed without protein enzymes—the Catch-22.

The Catch-22 conundrum dogged origin of life research for decades. Like DNA, since RNA contains information. The discovery that certain RNA molecules also have enzyme activity to self-replicate paved the way to solving the Catch-22 puzzle. RNA acts like a protein at times, and at times like DNA.

The RNA World theory has emerged as the most popular natural mechanism for the origin of life. The National Science Foundation (NSF) now actively promotes the RNA World theory. NSF is a United States government agency; its medical counterpart is the National Institutes of Health.  

In association with Harvard University, the NSF RNA World theory initiative now exists for “Synthesizing Darwinian Chemical Systems.” Under the direction of Jack Szostak from the Center for Computational & Integrative Biology, Gerald Joyce from The Scripps Research Institute, and Steven Benner from The Foundation for Applied Molecular Evolution state -

“As both a storehouse of genetic information and a catalyst of metabolic reactions, RNA may have been the critical component that enabled the evolution of life”

The RNA World concept started in 1959 when Spanish Catalan biochemist Joan Oró synthesized adenine, a key component of RNA and DNA, from hydrogen cyanide, similar to a Miller–Urey experiment at high temperatures.

By the late in the twentieth century, origin of life researchers began to examine the RNA World theory. American physicist, biochemist, and molecular biology pioneer Walter Gilbert, in 1986, was the first to coin the term “RNA World” 

Gilbert envisioned a RNA-first model on primordial Earth. By the actions of natural selection on RNA, DNA and protein molecules theoretically formed with the DNA molecule evolving into an information role, the protein molecules evolving into a catalytic role.

Like the Miller–Urey experiment though, the lack of geological evidence for hydrogen cyanide in the fossil record emerged as a telltale sign. Even worse, hydrogen cyanide is a gas toxic to cellular metabolism. During the German Nazi regime, hydrogen cyanide was the gas-of-choice at Auschwitz.

To date, not one laboratory experiment with realistic early Earth elements and conditions has produced a single nucleic acid. In 1981, Francis Crick published Life Itself, a book critical of the RNA World theory. “It may turn out that we will eventually be able to see how this RNA world got started” Crick later wrote in 1993. “At present, the gap from the primal ‘soup’ to the first RNA system capable of natural selection looks forbiddingly wide”

Scripps Research Institute biochemist Gerald Joyce states that the “most reasonable interpretation is that life did not start with RNA.” The origin of life is so difficult a problem that German researcher Klaus Dose stated in 1988 that the RNA theory is “a scheme of ignorance. Without fundamentally new insights in evolutionary processes … this ignorance is likely to persist.”

Origin of life scientist, Robert Shapiro from New York University, a RNA World critic, notes – “no nucleotides of any kind have been reported as products of spark-discharge experiments or in the studies of meteorites.”

Stanley Miller, who performed the original Miller-Urey prebiotic simulation test points out problems with Oro’s simulation – “a high temperature origin of life involving these compounds [the RNA bases] therefore is unlikely.” The presumption of “bases, adenine, cytosine, guanine and uracil were readily available on the early earth,” Miller continues, is “not supported by existing knowledge of the basic chemistry of these substances.”

At the Salk Institute for Biological Studies, Leslie Orgel in 1994 noted – “Because synthesizing nucleotides and achieving replication of RNA under plausible prebiotic conditions have proved so challenging, chemists are increasingly considering the possibility that RNA was not the first self replicating molecule…”.

NASA lost enthusiasm for the RNA world, as well. In the Final Report issued after the “Astrobiology Workshop” in 1996 at Ames Research Center, California, concluded –

“It has been postulated that there was a time in protobiological evolution when RNA played a dual role as both genetic material and a catalytic molecule (“the RNA world”). However, this appealing concept encounters significant difficulties. RNA is chemically fragile and difficult to synthesize abiotically. The known range of its catalytic activities is rather narrow, and the origin of an RNA synthetic apparatus is unclear.”

“It goes without saying that the emergence of this RNA world and the transition to a DNA world imply an impressive number of stages, each more improbable than the previous one”, noted the eminent François Jacob in 1997 

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

After 150 years running, how life spontaneously began, to which Darwin alluded, remains a mystery. The deputy editor of the journal Nature, and science writer, Nicholas Wade, reported in the New York Times in June 2000 “everything about the origin of life on the Earth is a mystery, and it seems the more that is known, the more acute the puzzle gets.”

Nearly twenty years later after Gilbert introduced the RNA World theory, the role of RNA in the origin of life remains elusive, if not improbable. In 2007, commenting in Proceedings of the National Academy of Sciences of the United States of America on a paper by Phillipp Baaske, Eugene V. Koonin, Senior investigator at the National Center for Biotechnology Information, National Library of Medicine, and National Institutes of Health noted -

“[RNA World] still is a hypothetical entity… the evolutionary path to the translation systems remains essentially uncharted.”

Richard Dawkins premise in The Ancestor’s Tale – “This is the RNA World. To see how plausible it is” – demonstrates how the common practice of word slighting in the evolution industry. The veiling of impossible as “plausible” reaches the edge of fraud—supported by US tax dollars.

In a letter to Sir Joseph Dalton Hooker, his closet friend in 1857, Charles Darwin confided,

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 the wake of the article published in Science on May 7, 2010, entitled “A Draft Sequence of the Neanderthal Genome”, the Smithsonian Institute is definitely destined for a very busy summer updating the fiasco at the Human Origins exhibit.

The reason is the research team led by geneticist Svante Pääbo at the Max-Planck Institute for Evolutionary Anthropology in Germany that wrote the article has discovered that the Neanderthals are indistinguishable from humans—Neanderthals and humans are the same species. John Hawks, assistant professor of anthropology at the University of Wisconsin, told BBC News: “They’re us. We’re them.”

Geneticist Gregory Hannon commenting on the historical event noted – the “publication of the full Neandertal genome is a watershed event, a major historical achievement.” The evidence from “A Draft Sequence of the Neanderthal Genome,” clearly contradicts the Human Origin exhibit at the Smithsonian Institute.

 The now evident fiascos at the Smithsonian Human Origin exhibit destined for updating include the following statements:

The Neanderthal sequences were substantially different from modern human mtDNA.

These results confirmed the earlier study that showed that Neanderthals were unlikely to have contributed to the modern human genome.

Neanderthals and modern humans were separate species.

“[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.”

By definition, different species cannot develop interbreeding populations, therefore the Neanderthals can no longer be considered ancestral to humans – because they are simply humans.

Clearly, the Smithsonian exhibit had presented Neanderthals as a missing link to humans not on scientific evidence, but on an evolutionary paradigm—a saga that continues as a ubiquitous plague.

 In using logic rather than scientific evidence, the Smithsonian exhibit theorized that humans and Neanderthal represents the missing link to humans because they were not interbreeding populations—a gamble that was lost.

More glaring fiascos destined for updating at the Smithsonian include the following statements:

They did not find a match between derived alleles or gene forms in modern humans and those in Neanderthals, which is evidence against interbreeding.

The preliminary sequence shows no evidence that Neanderthals and modern humans interbred.

Also, since studies show that Neanderthal mtDNA and Y chromosomes are very different, it is unlikely that Neanderthals and modern humans were interbreeding.

The exhibit exemplifies a greater fiasco to the evolutionary movement in which ideology has replaced science. With a long legacy of wrong theories and fraud, hopefully the Smithsonian will update the Human Origin exhibit based on scientific evidence—not an ideological agenda.

The immediate addressing of the Neanderthal fiasco will avoid the “fraud” label and not become the U.S. version of the Piltdown man.   

Just three years before the publication of The Origin of Species, in 1856, the first Neanderthal fossils were discovered in the Neander Valley limestone quarry located in Germany.  

In The Descent of Man, however, Darwin argued against the concept that the Neanderthals were the ancestors to humans based on the larger size of the Neanderthal skull.

“Nevertheless,” Darwin noted, “it must be admitted that some skulls of very high antiquity, such as the famous one of Neanderthal, are well developed and capacious”—the skull was too large to be a human ancestor.

Darwin was right. The journal Science on May 7, 2010, published an article entitled “A Draft Sequence of the Neandertal Genome,” confirming Darwin’s position that the Neanderthal could not be an ancestor to humans. According to Gregory Hannon of Cold Spring Harbor Laboratory in Laurel Hollow, N.Y., the “publication of the full Neandertal genome is a watershed event, a major historical achievement.” 

Svante Pääbo of the Department of Evolutionary Genetics at the Max-Planck Institute for Evolutionary Anthropology in Germany led the study team. “[Neanderthals] are not totally extinct,” Pääbo said. “In some of us they live on, a little bit.”

John Hawks, assistant professor of anthropology at the University of Wisconsin, told BBC News: “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.”

This interbreeding finding is a monumental discovery since interbreeding is a defining factor for defining a species. Our current modern definition of species was developed by Ernst Mayr—Darwin’s Bulldog of the twentieth century.

In the 1942 book entitled Systematics and the Origin of Species, Ernst Mayr established the Biological Species Concept (BSC): species consist of populations of organisms that can reproduce with one another and are reproductively isolated from other such populations. Since humans and Neanderthals are now known to be isolated reproductive populations, they represent a single species—”They’re us. We’re them.”

Sequencing of the Neanderthal genome is a landmark scientific achievement. The sequencing is a culmination of a four-year investigation led from Germany’s Max Planck Institute.

Use of efficient “high-throughput” technology allowed the numerous DNA sequences to be processed at the same time from the bones of three different Neanderthals found at Vindija Cave in Croatia.

A major obstacle overcome in the study was the retrieval of quality DNA material from remains Neanderthal DNA contaminated with vast quantities of bacterial and fungal DNA. Even, the Neanderthal DNA had broken down into very short segments and had changed chemically. Since the contamination, breaks, and chemical changes were thought to be of a predictable nature, the researchers developed a software program to estimate the original DNA sequence of the Neanderthal genes.

The DNA evidence from the Neanderthal clearly aligns with the biblical account—the Neanderthals are human, descendants of Adam and Eve. Worldwide dispersion after Babel followed by environmental pressures afterward resulted in people groups with different physical characteristics, including humans with “Neanderthal” Characteristics.

Cellular biologist, David DeWitt, noted that the research was an “amazing feat” of science that continues to demonstrate the validity of the biblical record. “Finding Neanderthal DNA in humans was not expected by evolutionists, but it was predicted from a creation standpoint because we have said all along that Neanderthals were fully human: descendants of Adam and Eve just like us”.