Posts Tagged ‘genome’

The long-awaited genome analysis for one of the most infamous fish in evolution history, the coelacanth, was published last week by lead scientists Chris T. Amemiya of University of Washington, and Jessica Alföldi from MIT and Harvard in the prestigious journal Nature.  

The coelacanth, first described in 1839 by Louis Agassiz at Harvard University, has played a pivotal role in the history of evolution. Based on the early fossil evidence, the coelacanth had long been thought to be an extinct evolutionary link in the transition between the fish and amphibians, also known as tetrapods. The coelacanth was touted as a fin-to-limb transition link.

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The newly discovered Mimivirus is proving to be a challenging to the basic fundamentals of the evolution of microbe to man tree of life.

The Mimivirus was serendipitously discovered in 1992 while researching Legionellosis, a potentially fatal infectious disease caused by a bacteria belonging to the genus Legionella. Since the new organism appeared to be a bacterium, it was originally named Bradfordcoccus after the city where it was discovered, Bradford, England. Continue Reading

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”. Continue Reading

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.

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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.

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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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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 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.

The anticipation around Charles Darwin’s 200^th birthday celebration passed nearly unnoticed. Few media venues ventured to highlight the day. Perhaps, the struggling economy naturally selected the sullenness.

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.