Archive for May, 2010

Chimp Genetics Radically Different

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)

First Synthetic Species

While evoking images of Frankenstein-like scientific tinkering, this week J. Craig Venter of the Craig Venter Institute in Rockville, Md said,

We’re here to announce the first synthetic cell.

Venter told reporters that the new species — dubbed Mycoplasma mycoides JCVI-syn1.0 — is similar to one found in nature, but each cell is controlled only by a single million-base pair chromosome assembled from the bio-computer laboratory. The research is reported in the May 20 issue of Science.

The new species, Venter said, started with researchers digitizing the genetic code for the new species on computers, and then assembling the nucleotides using “four bottles of chemicals” into sections of DNA. The DNA sections were assembled in yeast cells to form a synthetic chromosome, which was then transferred to a related species of bacteria, M. capricolum.

Late in March, the researchers told reporters, the modified cells began replicating and formed a “blue colony” of the new species. Venter said,

This is the first self-replicating species that we’ve had on the planet whose parent is a computer.

Indeed, he and his colleagues consistently used computer language to describe the work. The new chromosome is like an operating system, they said, and it reprograms the M. capricolum cells to become M. mycoides.

The result comes after 15 years of research — and some $40 million — aimed at finding what Venter has called the minimal genome: the smallest set of genes that can support a living creature. But it could quickly have spinoffs, the researchers said.

This process has enormous commercial potential, including new tools for developing future vaccines, pharmaceuticals, biofuels, biochemicals, and perhaps synthetic algae to cope with oil spills such as the one currently threatening the Gulf Coast of the U.S.

Describing the new species as “synthetic” may be going too far, according to some experts. It’s “synthetic in the sense that its DNA is synthesized, not in that a new life form has been created,” according to molecular biologist Jim Collins of Boston University writing in the Nature. “Its 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, Ore., also writing in the Nature commentary called the new species “a normal bacterium with a prosthetic genome.”

The prosthetic genome had some problems, however. Venter and colleagues were stalled for several months because one of the pieces of DNA they painstakingly crafted had a typo – a single base-pair deletion – that means the whole chromosome could not function.

“So accuracy is essential,” Venter said. “There’s parts of the genome where it can’t tolerate even a single error and there’s parts where we can put in large blocks of DNA and it can tolerate all kinds of errors.”

Molecular geneticist Georgia Purdom from Ohio State University noted that this 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.”

Regardless of the inference to molecules-to-man evolution, even Venter noted that they “didn’t create life from scratch.”

Frances Arnold, synthetic biologist at the California Institute of Technology in Pasadena, emphasized “[w]e can write anything we want,” said Arnold. “The problem is that we don’t know what to write.”

This historical event highlights the fact that writing genetic information has an absolute requirement—intelligence with perfection.

 

Jonathan Wells of the Discovery Institute explains further what’s going on behind the headlines at Evolution News & Views:

Smithsonian Human Origin Fiasco

 

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.   

Darwin, DNA, and the Neanderthals

 

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”.

Offer of a Lifetime

 

After a flurry of studying, in January of 1831, at the age of twenty-one, Charles Darwin passed his examination for the Bachelor of Arts in theology, Euclid, and the classics from the University of Cambridge—finishing tenth out of a field of 178.

Remaining at Cambridge for two more terms after passing the final examination, Darwin became obsessed with the desire to travel. As a stroke of fate, after returning from a geological surveying tour in Wales was a letter from Professor John Henslow, with the offer of a lifetime. Darwin wrote,

“On returning home from my short geological tour in N. Wales, I found a letter from Henslow, informing me that Captain Fitz-Roy was looking for any young man who would volunteer to go with him without pay as naturalist to the voyage of the Beagle.”

The voyage was a planned two-year expedition to chart the coastline of South America in December. When Darwin shared the letter, his father said, “If you can find any man of common sense who advises you to go I will give my consent.” Not knowing who to ask, on August 31, 1831, Darwin wrote a letter to Henslow reluctantly turning down the offer.

By pure coincidence on the next day, Josiah Wedgwood II, Darwin’s uncle, arrived to visit Darwin’s father. Since Josiah was considered “one of the most sensible men in the world” by his father, Darwin discussed the situation with Josiah, who immediately made the case for the expedition.

Sealing the deal, Josiah offered to pay Darwin’s cost for the planned two-year expedition—an expedition that would eventually stretch to nearly five years. The next day Darwin quickly left for Cambridge to meet with Henslow to intercept the letter he had just sent.

On September 5, 1831, Henslow introduced Darwin to FitzRoy in London. FitzRoy was a wealthy nobleman, a descendant of the Duke of Grafton, and the Marquis of Londonderry. He was widely admired for his tight reign on his men, but as Darwin was soon to discover, his commanding was accompanied by a fiery temper.

At the age of twenty-six, FitzRoy, not much older than Darwin was at first, FitzRoy was not impressed with Darwin. FitzRoy thought the shape of Darwin’s nose was too weak to take a lengthy sea voyage. Eventually, Captain FitzRoy was persuaded—Henslow’s recommendation was accepted.

Darwin was appointed to be a “gentleman’s naturalist” and assist the “official” naturalist, surgeon Robert McKormick. As a paying passenger, Darwin was granted full use all the onboard facilities to perform research as a naturalist. Darwin was set to begin his life-long dream—exploring the tropics.

FitzRoy outlined the details of the voyage, including the impending sail date, October 10. Not wasting any time, Darwin took up residence at 17 Spring Gardens in London and began shopping and discussing the details of the voyage with FitzRoy; a dynamic relationship had just been launched.

Convinced “that he would find scientific proof that Genesis was literally true,” FitzRoy wanted a like-minded naturalist on board the Beagle to find the evidence. Darwin’s interest in William Paley’s perspective on nature made Darwin the perfect applicant. Paley’s book, Evidences of Christianity, espoused a divine design in nature.

Ironically, prior to leaving England, FitzRoy gave Darwin a copy of the just-released first volume of Charles Lyell’s new theory in the book entitled Principles of Geology, which argues in favor of only slight, successive changes in the earth. Lyell championed geological uniformitarianism. The tenet of uniformitarianism is that all the events over the history of the Earth are the same as today—catastrophic events on Earth, like The Flood and plate tetonics never happened.

Little did FitzRoy know that Principles of Geology would influence the impressions of Darwin to challenge rather than support the Genesis account. Although Darwin struggled to understand how the massive land movements along western coast of South America aligned with uniformitarianism, Darwin never abandoned Lyell’s theory.

The offer of a lifetime lead to the development of a lifetime pattern for Darwin—theory development contradicted by the evidence. Or as Charles Darwin’s brother, Erasmus, put it in a letter to Charles on November 23,1859, one day before the publication of The Origin of Species – “if the facts won’t fit, why so much the worse for the facts, in my feeling.”

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Darwin, Then and Now is a journey through the most amazing story in the history of science - the history of evolution. The book encapsulates who Darwin was, what he said, and what scientists have discovered since the publication of The Origin of Species in 1859.

With over 1,000 references, Darwin Then and Now is a historical chronicle of the rise and fall of the once popular theory of biological evolution.

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