Archive for the ‘PopEvo News’ Category

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:

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.   

Jerry A. Coyne, one of the leading evolutionists at the University of Chicago, in his new book entitled Why Evolution is True (2009) writes “much confusion and misunderstanding surrounds evolution” even though “the modern theory is easy to grasp.” The question is how can a theory be “easy to grasp” and still be surrounded by “much confusion”?

But what could the confusion be over? Here are some examples.  Charles Darwin wrote in The Origin of Species - “There is no logical impossibility in the acquirement of any conceivable degree of perfection through natural selection”. Coyne contradicts Darwin by stating – “natural selection does not yield perfection”. Over a trivial issue, confusion reigns over whether natural selection can or cannot produce perfection in nature.

Presumably, to show how easy the theory of evolution is to understand, Coyne features what he calls the six basics of evolution: “evolution, gradualism, speciation, common ancestry, natural selection, and nonselective mechanisms”. For Coyne, natural selection is not the exclusive driving force of evolution.

Niles Eldredge, evolutionary biologist and curator of the American Museum of Natural History, disagrees. Niles Eldredge, architect  and designer of the museum’s currently touring Darwin exhibit in the companion book Darwin, Discovering the Tree of Life (2005), credits Darwin with discovering the actions of natural selection—the essence of evolution: “When [Darwin] formulated the principle of natural selection, he had discovered the central process of evolution.”

Unlike Coyne, Eldredge envisions evolution acting exclusively through the process of natural selection: “A century and a half ago, Charles Darwin offered the world a single, simple scientific explanation for the diversity of life on Earth: evolution by natural selection.” Unlike Coynes six basics of evolution, Eldredge uses a VISTA acronym for natural selection that stands for Variation, Inheritance, Selection, Time, and Adaptation.

Differences in approach even between Coyne and Eldredge, exemplify why evolution theory continues to be confusing—even on the basics. The teaching of evolution is in chaos. Coyne pines “most of my university students who supposedly learned evolution in high school, come to my courses know almost nothing about this central organizing theory of biology.” Could it be because a unified theory of evolution simply does not exist?

Even university science major graduates seem to be no better. T. Ryan Gregory and Cameron A. J. Ellis, in their paper entitled “Conceptions of Evolution Among Science Graduate Students” published in BioScience 59(9):792-799 (2009), surprizingly found that less than 30% of students pursuing advanced science degrees could correctly identify even the basic principles of evolution.

The reason is—a comprehensive theory of evolution simply does not exist. Even with the convening of the most respected evolutionary scientists at the Altenberg Summit in 2008, no consensus was reached on a comprehensive theory of evolution.

Given the flood of available evidence, in the wake of Crick’s Central Dogma collapse, evolution is a theory that remains in chaos—now more than ever.

Evolution is a theory in crisis. Even students pursuing advanced degrees in science cannot grasp the basics of evolution, according to a new study by University of Guelph researchers.

The finding reveals evolutionary teaching is in chaos from elementary school up, said Ryan Gregory, a professor in Guelph’s Department of Integrative Biology, who conducted the research with former student Cameron Ellis.

The study was published in BioScience and is particularly timely, given that this year is the bicentennial of Charles Darwin’s birth and the 150th anniversary of publication of On the Origin of Species, which underpins understanding of the diversity of Earth’s organisms and their interrelations.

“Misconceptions about natural selection may still exist, even at the most advanced level,” Gregory said.

“We’re looking at a subset of people who have spent at least four years, sometimes even six or seven years, in science and still don’t necessarily have a full working understanding of basic evolutionary principles or scientific terms like ‘theories.’”

Many previous studies have assessed how evolution is understood and accepted by elementary, high school and undergraduate students, as well as by teachers and the general public, Gregory said. But this was the first to focus solely on students seeking graduate science degrees.

The study involved nearly 200 graduate students at a mid-sized Canadian university who were studying biological, physical, agricultural, or animal sciences. When the students were asked to apply basic evolutionary principles, only 20 to 30 per cent could do so correctly, and many did not even try to answer such questions. Of particular interest to Gregory was the finding that many students seem less than clear about the nature of scientific theories.

“This is telling us that traditional instruction methods, while leading to some basic understanding of evolution, are not producing a strong working knowledge that can be easily applied to real biological phenomena.”

The outcome underscores the failure of single cohesive theory of evolution to emerge since the collapse of evolution’s Central Dogma at the turn of the century. Ryan Gregory’s study further demonstrates that education on an non-cohesive theory leads to chaos in the schoolhouse.  

A British film about Charles Darwin has failed to find a US distributor because his theory of evolution is too controversial, according to its producer. 

The film entitled Creation, starring Paul Bettany, details Darwin’s “struggle between faith and reason” as he wrote On The Origin of Species. It depicts him as a man who loses faith in God following the death of his beloved 10-year-old daughter, Annie.

The film was chosen to open the Toronto Film Festival and has its British premiere this Sunday, September 20. Creation was developed by BBC Films and the UK Film Council. US distributors, however, have resolutely passed on the film. The film has sparked fierce debate because of Darwin’s known influence on the wave of twentieth century social engineering struggles, and more simply, the convergence physical of evidence has failed to support Darwin’s theory after 150 years. 

Movieguide.org, described Darwin as the father of eugenics and denounced him as “a racist, a bigot and an 1800s naturalist whose legacy is mass murder”. His “half-baked theory” directly influenced Adolf Hitler and led to “atrocities, crimes against humanity, cloning and genetic engineering”, the site stated. According to a Gallup poll conducted in February, only 39% of Americans believe in the theory of evolution.

Had pre-production marketing not been so far off-target, Jeremy Thomas, the Oscar-winning producer of Creation, would not have been so stunned and left wondering why “People have been saying this is the best film they’ve seen all year, yet nobody in the US has picked it up.”

With the evaporation of the Central Dogma of evolution, there has been a resurgencent interest in Charles Darwin’s forerunner, Jean-Baptiste Lamarck and the Lamarckian theory of evolution. Epigenetics and Larmackian experimentalists are the new trend.  

Darwin was on target stating, “Lamarck, who believed in an innate and inevitable tendency towards perfection in all organic beings, seems to have felt this difficulty so strongly that he was led to suppose that new and simple forms are continually being produced by spontaneous generation. Science has not as yet proved the truth of this belief.”

Ida brands frenzied media blitz, an expose for “The Year of Darwin.” Malcolm Ritter of the Associated Press reported, “Scientists say they’ve found a “missing link.”

 On May 10, 2009, the Daily Mail published reports that the BBC had made a documentary revealing the discovery of what might be a vital ‘missing link’ in human evolution, giving an outline of the study and its intended publication date as well as a brief statement. On 15 May the Wall Street Journal carried a report with interviews, who cautioned that “Lemur advocates will be delighted, but tarsier advocates will be underwhelmed.” Around the same time, a press release headed “World Renowned Scientists Reveal a Revolutionary Scientific Find That Will Change Everything” announced that the find was “lauded as the most significant scientific discovery of recent times.”

 On May 19, 2009, the Ida investigative team headed by Jens Franzen revealed their findings to the world at a press conference, simultaneously with online publication of the paper in PLoS ONE. At the press conference, the fossil was described as the “missing link” in human evolution, and “This fossil rewrites our understanding of the evolution of primates… It will probably be pictured in all the textbooks for the next 100 years.”

 The authors and compared its importance to the Mona Lisa. The authors also said that Darwinius was “the closest thing we can get to a direct ancestor” and that finding it was “a dream come true”. Team member Dr Jens Franzen said the state of preservation was “like the Eighth Wonder of the World”, with information “palaeontologists can normally only dream of”, but while he said it bore “a close resemblance to ourselves” in some aspects, other features indicated that it was not a direct ancestor.

 The Franzen team should have searched for a more definitive conclusion; experts were quick to counter.

 Henry Gee, a senior editor at Nature, said the term “missing link” was misleading and that the scientific community would need to evaluate its significance.

“The PR campaign on this fossil is I think more of a story than the fossil itself,” said anthropologist Matt Cartmill of Duke University in North Carolina. “It’s a very beautiful fossil, but I didn’t see anything in this paper that told me anything decisive that was new.”

 Chris Beard, curator of the Carnegie Museum of Natural History, said he “would be absolutely dumbfounded if it turns out to be a potential ancestor to humans.”^[

 “It’s not a missing link, it’s not even a terribly close relative to monkeys, apes and humans, which is the point they’re trying to make,” Carnegie Museum of Natural History curator of vertebrate paleontology Chris Beard said.

Ann Gibbons in “Revolutionary’ Fossil Fails to Dazzle Paleontologists” and published in ScienceNOW noted, “Many paleontologists are unconvinced.”

 Robert Roy Britt writing “Ida Fossil Hype Went Too Far” in LiveScience noted, “Problem is, most of the coverage is done, and the public could be left with the impression that Ida is a rock-solid missing link in the human evolutionary chain.”

 Ida’s unveiling was highly scripted with some “Barnum and Bailey aspects,” said paleontologist Richard Kay of Duke University. Britt continued, “More important, it can now be said the findings may well have been significantly overstated. We won’t know for sure until further research is done. But if this event causes the public to distrust science and media, that distrust is well placed.”

Gary Marcus, professor of psychology at New York University and author of “Kluge: The Haphazard Evolution of the Human Mind”, in the Opinion section of Wall Street Journal February 11, 2009 writes, “Neither evolution nor Darwin ever promised anything like perfection.”

 Yet, in percieving perfection in nature, Darwin wrote, “the belief that an organ so perfect as the eye could have been formed by natural selection is enough to stagger any one.” Darwin suggested, “There is no logical impossibility in the acquirement of any conceivable degree of perfection through natural selection.”

 Marcus may have been confused, since Darwin was confused had contradicted himself by writing in The Origin of Species, “Natural selection will not produce absolute perfection, nor do we always meet, as far as we can judge, with this high standard under nature.”

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.