We wuz wrong! Darwinist claim about 500 million year old gene was way shoddier than we thought …

_{Denyse O'Leary

July 13, 2012

Darwinism, Intelligent Design}

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Jonathan Wells, author of The Myth of Junk DNA, gives us the lowdown on the recent ScienceDaily announcement, “Giving Ancient Life Another Chance to Evolve: Scientists Place 500-Million-Year-Old Gene in Modern Organism.” [1] (which we covered here.)

He writes,

But this announcement is extremely misleading, and typical of the shameless hype that so often accompanies breaking news in evolutionary biology.

The so-called “500-million-year-old gene” is an artificially engineered DNA sequence based on an inference from a hypothetical phylogenetic tree about what the ancestral sequence might have been. The procedure was this: Two groups of evolutionary biologists constructed hypothetical phylogenetic trees of bacteria, based on similarities and differences in their DNA [2,3].

A third group inferred from these hypothetical trees the DNA sequence of what they believed to be the ancestral version of a particular gene [4], and the group featured by Science Daily “resurrected” the hypothetical ancestral gene by synthesizing its inferred DNA sequence in the laboratory.

The artificial gene was not 500 million years old. In fact, its inferred DNA sequence, like the phylogenetic trees on which the inference was based, depended heavily on the neo-Darwinian assumptions with which the researchers began. Like so much other arguments for Darwinian evolution, this began by assuming evolution is true.

[1] “Giving Ancient Life Another Chance to Evolve: Scientists Place
500-Million-Year-Old Gene in Modern Organism,” Science Daily (July 11,
2012). http://www.sciencedaily.com/releases/2012/07/120711100726.htm

[2] Battistuzzi FU, Feijao A & Hedges SB, “A genomic timescale of prokaryote
evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land. BMC Evolutionary Biology 4 (2004): 44. http://www.biomedcentral.com/1471-2148/4/44

[3] Ciccarelli FD, Doerks T, von Mering C, Creevey CJ, Snel B & Bork P, “Toward automatic reconstruction of a highly resolved tree of Life,” Science 311 (2006): 12831287.

[4] Gaucher EA, Govindarajan S & Ganesh OK, ³Palaeotemperature trend for Precambrian life inferred from resurrected proteins,² Nature 451 (2008): 704-707.

Does anyone know what Darwinists would do if it occurred to them that Darwinism is nonsense?

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Comments

BA77 is once again logically incoherent.
But as far as this giving any comfort to Darwinism, well it certainly doesn’t do that because #1, the sequence was arrived at by concerted intelligence
I got it now. If scientists don't re-trace the steps of evolution, that proves evolution cannot happen in nature. If scientists do re-trace the steps of evolution, that proves evolution cannot happen in nature, because all their experiments are "intelligently designed." If scientists can't reproduce evolution in the lab, that disproves evolution. If scientists can reproduce evolution in the lab, that also disproves evolution.
and #2, ancient genes are apparently ‘more evolved’ than modern strains!
BA77 is not paying attention. The new bacteria did not become fitter in the modern environment by mutating the old protein. They became fitter by mutating their current proteins. This tells us exactly zero about whether the old protein is more or less "evolved." And the concept of more or less "evolved" means nothing except relative to a particular environment. Fitness is always relative to an environment. The bacteria are now in a completely different environment than they used to be, so you can't measure the "fitness" of this old protein. Bacteria that evolve resistance to antibiotics are always fitter-- more "evolved" if you will-- than wild-type bacteria in an environment with antibiotics. Scientists have observed many examples of evolution involving gains in complexity and evolution of novel biochemical functions, including the processing of xenobiotics. A vast literature there. Sorry, it's real science not YouTube videos.Diogenes_{July 18, 2012
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Maybe Wells could explain why, if the assumptions involved in reconstructing the ancient sequence are nonsense, the resulting sequence functions at all. If he is right that the procedure is nonsense, then the differences in the derived sequence and modern sequences would amount to a bunch of random changes, which should, if they are substantial, result in a non-functional protein.PNG_{July 17, 2012
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Hi BA77, I wasn't able to watch the video, but I'm guessing that there is some standard fitness test that biologists use to measure and compare different bacteria. Okay, so the bacteria with the "ancient" gene is at first less fit than present day bacteria, But then many of the modern day genes, but not the "ancient" gene, mutate until some strains of the hybrid bacteria are more fit than present day bacteria. So your interpretation is that the "ancient" gene contained more information (less entropy), which it passed on to the other genes somehow? The example of the fitness of bacteria from ancient insects that you cite seems to support your view. I would be curious to know what would happen if scientists continue to re-create "ancient" genes and find that they result in higher fitness levels. Would that overturn mainstream evolutionary views or not? Your additional information about the lack of evolution of cyanobacteria and the other kinds of bacteria are interesting, but I don't see the connection to your point about genetic entropy.Bilbo I_{July 13, 2012
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Well Bilbo, here is the article as it appeared on Science Daily
Giving Ancient Life Another Chance to Evolve: Scientists Place 500-Million-Year-Old Gene in Modern Organism - July 11, 2012 Excerpt: After achieving the difficult task of placing the ancient gene in the correct chromosomal order and position in place of the modern gene within E. coli, Kaçar produced eight identical bacterial strains and allowed "ancient life" to re-evolve. This chimeric bacteria composed of both modern and ancient genes survived, but grew about two times slower than its counterpart composed of only modern genes. "The altered organism wasn't as healthy or fit as its modern-day version, at least initially," said Gaucher, "and this created a perfect scenario that would allow the altered organism to adapt and become more fit as it accumulated mutations with each passing day." The growth rate eventually increased and, after the first 500 generations, the scientists sequenced the genomes of all eight lineages to determine how the bacteria adapted. Not only did the fitness levels increase to nearly modern-day levels, but also some of the altered lineages actually became healthier than their modern counterpart. When the researchers looked closer, they noticed that every EF-Tu gene did not accumulate mutations. Instead, the modern proteins that interact with the ancient EF-Tu inside of the bacteria had mutated and these mutations were responsible for the rapid adaptation that increased the bacteria's fitness. In short, the ancient gene has not yet mutated to become more similar to its modern form, but rather, the bacteria found a new evolutionary trajectory to adapt. http://www.sciencedaily.com/releases/2012/07/120711100726.htm
Modern day bacteria which have mutations to become resistant to antibiotics are well known for their inability to pass what is termed a 'fitness test' against a non-mutated strain of bacteria. i.e. The mutated strain is less robust for survival than the the non-mutated strain. This fact is one fact that has argued very strongly against Darwinian evolution since no one can seem to find any examples of complexity increasing above what is already present in the bacteria. Which is what made the preceding finding very interesting. They seems very likely that they must have somehow hit on a right, "pristine", genetic sequence that had not been slowly deteriorated through supposed millions of years of 'genetic entropy' in order to pass the notoriously difficult fitness test against the modern strain. It simply doesn't make sense otherwise.,,, But as far as this giving any comfort to Darwinism, well it certainly doesn't do that because #1, the sequence was arrived at by concerted intelligence and #2, ancient genes are apparently 'more evolved' than modern strains! :) i.e. they have empirical proof of Darwinism in reverse, genetic entropy of modern strains! notes: Here is a video of the 'Fitness Test' that evolutionary processes have NEVER passed as for a demonstration of the generation of functional complexity/information above what was already present in a parent species bacteria:
Is Antibiotic Resistance evidence for evolution? - 'Fitness Test' - video http://www.metacafe.com/watch/3995248 List Of Degraded Molecular Abilities Of Antibiotic Resistant Bacteria: http://www.trueorigin.org/bacteria01.asp
Moreover, the molecular sequences of ancient bacteria are very similar to modern sequences:
The Paradox of the "Ancient" (250 Million Year Old) Bacterium Which Contains "Modern" Protein-Coding Genes: “Almost without exception, bacteria isolated from ancient material have proven to closely resemble modern bacteria at both morphological and molecular levels.” Heather Maughan*, C. William Birky Jr., Wayne L. Nicholson, William D. Rosenzweig§ and Russell H. Vreeland ; http://mbe.oxfordjournals.org/cgi/content/full/19/9/1637
Evolutionists were so disbelieving at this stunning lack of change, far less change than was expected from the neo-Darwinian view, that they insisted the stunning similarity was due to modern contamination in Vreeland's experiment. Yet the following study laid that objection to rest by verifying that Dr. Vreeland's methodology for extracting ancient DNA was solid and was not introducing contamination because the DNA sequences this time around were completely unique:
World’s Oldest Known DNA Discovered (419 million years old) - Dec. 2009 Excerpt: But the DNA was so similar to that of modern microbes that many scientists believed the samples had been contaminated. Not so this time around. A team of researchers led by Jong Soo Park of Dalhousie University in Halifax, Canada, found six segments of identical DNA that have never been seen before by science. “We went back and collected DNA sequences from all known halophilic bacteria and compared them to what we had,” Russell Vreeland of West Chester University in Pennsylvania said. “These six pieces were unique",,, http://news.discovery.com/earth/oldest-dna-bacteria-discovered.html
Genetic Entropy explains why completely unique sequences would be lost:
Professor's hypothesis may be game changer for evolutionary theory - April 2012 Excerpt: "According to the hypothesis, evolution pushes microorganisms to lose essential functions when there is another species around to perform them. This idea counters popular evolutionary thinking that living organisms evolve by adding genes rather than discarding them.,, "A common assumption about evolution is that it is directed toward increasing complexity," said Erik Zinser, associate professor of microbiology. "But we know from analysis of microbial genomes that some lineages trend toward decreasing complexity, exhibiting a net loss of genes relative to their ancestor." http://www.physorg.com/news/2012-04-professor-hypothesis-game-changer-evolutionary.html
Related work on ancient bacteria here;
“Raul J. Cano and Monica K. Borucki discovered the bacteria preserved within the abdomens of insects encased in pieces of amber. In the last 4 years, they have revived more than 1,000 types of bacteria and microorganisms — some dating back as far as 135 million years ago, during the age of the dinosaurs.,,, In October 2000, another research group used many of the techniques developed by Cano’s lab to revive 250-million-year-old bacteria from spores trapped in salt crystals. With this additional evidence, it now seems that the “impossible” is true.” http://www.physicsforums.com/showthread.php?t=281961
Dr. Cano's work on ancient bacteria came in for intense scrutiny since it did not conform to Darwinian predictions, and since people found it hard to believe you could revive something that was millions of years old. Yet Dr. Cano has been vindicated:
“After the onslaught of publicity and worldwide attention (and scrutiny) after the publication of our discovery in Science, there have been, as expected, a considerable number of challenges to our claims, but in this case, the scientific method has smiled on us. There have been at least three independent verifications of the isolation of a living microorganism from amber."
In reply to a personal e-mail from myself, Dr. Cano commented on the 'Fitness Test' I had asked him about:
Dr. Cano stated: "We performed such a test, a long time ago, using a panel of substrates (the old gram positive biolog panel) on B. sphaericus. From the results we surmised that the putative "ancient" B. sphaericus isolate was capable of utilizing a broader scope of substrates. Additionally, we looked at the fatty acid profile and here, again, the profiles were similar but more diverse in the amber isolate.": Fitness test which compared ancient bacteria to its modern day descendants, RJ Cano and MK Borucki
This was extraordinary for me for I have never heard of the fitness test being passed, i.e. the most solid evidence available for the most ancient DNA scientists are able to find does not support evolution happening on the molecular level of bacteria. In fact, according to the fitness test of Dr. Cano, the change witnessed in bacteria conforms to the exact opposite, Genetic Entropy; a loss of functional information/complexity, since fewer substrates and fatty acids are utilized by the modern strains. Considering the intricate level of protein machinery it takes to utilize individual molecules within a substrate, we are talking an impressive loss of protein complexity, and thus loss of functional information, from the ancient amber sealed bacteria. related notes:
Static evolution: is pond scum the same now as billions of years ago? Excerpt: But what intrigues (paleo-biologist) J. William Schopf most is lack of change. Schopf was struck 30 years ago by the apparent similarities between some 1-billion-year-old fossils of blue-green bacteria and their modern microbial counterparts. "They surprisingly looked exactly like modern species," Schopf recalls. Now, after comparing data from throughout the world, Schopf and others have concluded that modern pond scum differs little from the ancient blue-greens. "This similarity in morphology is widespread among fossils of [varying] times," says Schopf. As evidence, he cites the 3,000 such fossils found; http://www.thefreelibrary.com/Static+evolution%3A+is+pond+scum+the+same+now+as+billions+of+years+ago%3F-a014909330 AMBER: THE LOOKING GLASS INTO THE PAST: Excerpt: These (fossilized bacteria) cells are actually very similar to present day cyanobacteria. This is not only true for an isolated case but many living genera of cyanobacteria can be linked to fossil cyanobacteria. The detail noted in the fossils of this group gives indication of extreme conservation of morphology, more extreme than in other organisms. http://bcb705.blogspot.com/2007/03/amber-looking-glass-into-past_23.html
bornagain77_{July 13, 2012
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It was "fitter" in relation to what, exactly? And in order to study the evolution of an ancient organism, wouldn't we need to study all the components of the organism together? Otherwise, wouldn't our results be rather skewed?Bilbo I_{July 13, 2012
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But the burning question remains, exactly why was the modern bacteria, that had the purported 500 myo ancient gene implanted, more fit than the modern strain that did not have the implanted gene (albeit after slow, less fit, start)? and exactly why did the implanted gene not mutate while the modern genes did mutate to accomodate the ancient gene to gain the fitness advantage over the non-altered modern strains of bacteria? It simply makes no sense. They must have done a little bit of something exactly right in order to get the correct information in the 'ancient' gene since, #1, non-functional sequences are so overwhelming prevalent and #2 the fitness actually did increase over modern strains (which is certainly not a minor matter).bornagain77_{July 13, 2012
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