Creationists sequence e coli genome

_{Denyse O'Leary

May 18, 2015

Genomics, Intelligent Design, News}

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Stuff we mustn’t tell Bill Nye (if anyone still cares where he is or what he is doing)

PubMed link for one e coli genome from Liberty University here.

Darwin followers free to call police.

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Comments

Pseudogenes are a classification rather than a literal definition.Dr JDD_{May 20, 2015
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I don't think that number is readily quantifiable, Mung. Luckily it's also of no relevance to the question of how much junk DNA there is in the human (or other Eukaryotic species) genome.wd400_{May 19, 2015
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Bob O'H: Probably very little – bacteria don’t tend to have a lot of junk DNA. And what percentage of all the DNA currently in existence is bacterial DNA?Mung_{May 19, 2015
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'scuse me! I should have Googled first. That was Regent University, Pat Robertson's University, that staffed Alberto Gonzales' Justice Dept. NOT Liberty U., which is Jerry Falwell's university.MatSpirit_{May 19, 2015
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I'm sure you know a lot more about biology than I do Bob, but when I read that they found 5268 genes and 305 pseudo genes, I assumed the pseudos were junk. I don't know about the 103 frame shifted genes. I understand some of those are occasionally useful. All in all, it looks like Liberty is training up a fine group of lab techs. And this is certainly not the disaster of Liberty's law school, as was revealed in the G. W. Bush admin.MatSpirit_{May 19, 2015
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Denyse, is this another example of your famous crowd sourcing, where you don't bother to read more than half of the headline of some press release, and ask your readers to fill in the rest? As daveS stated in the second comment: the title of this post should be Creationists sequence Citrobacter rodentium genomeOrloog_{May 19, 2015
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MatSpirit @ 6-
Homework assignment: How much junk DNA did the Liberty boys discover?
Probably very little - bacteria don't tend to have a lot of junk DNA.Bob O'H_{May 19, 2015
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Wd400, Hmmm. I wanted to debate. I'll just have to call you a big dummy and demand you retract your foolish comment!:)Collin_{May 18, 2015
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sure.wd400_{May 18, 2015
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wd400, Do you admit that there has been some faulty reasoning along these lines though? That when someone explains the benefits of a thing they assume they have explained the origins and cause of the thing?Collin_{May 18, 2015
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No. I mean if you want to understand a document one step you should consider taking is reading it. Or at leas the very first sentence. Otherwise you might look a bit silly. The headline seems fine to me -- persistence means continued existence, after all.wd400_{May 18, 2015
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wd400
You might try reading the first sentence of the press release…
I guess you're saying that we shouldn't expect evolutionists to be able to write an accurate headline. If so, I'm ok with that.Silver Asiatic_{May 18, 2015
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wd400 you state:
"it’s interesting to note how much evolutionary reasoning goes into the pipelines they used to do the annotation."
Precisely what 'evolutionary reasoning' in their paper are you referring to? Is it this 'evolutionary reasoning'?
"Mice are the preferred model for investigating human gastrointestinal disease because mice and humans have similar gastrointestinal tracts."
If so, then the mouse model is far less conducive too 'evolutionary reasoning' than you (and many others) seem to realize:
What scientific idea is ready for retirement? – Mouse Models Excerpt: A recent scientific paper showed that all 150 drugs tested at the cost of billions of dollars in human trials of sepsis failed because the drugs had been developed using mice. Unfortunately, what looks like sepsis in mice turned out to be very different than what sepsis is in humans. Coverage of this study by Gina Kolata in the New York Times incited a heated response from within the biomedical research community. AZRA RAZA – Professor of medicine and director of the MDS Centre, Columbia University, New York http://www.theguardian.com/science/2014/jan/12/what-scientific-idea-is-ready-for-retirement-edge-org Mouse gene expression reveals “widespread differences” from humans - Nov. 22, 2014 Excerpt: an international group of researchers has found powerful clues to why certain processes and systems in the mouse — such as the immune system, metabolism and stress response — are so different from those in people.,,, Mice are widely used to model human metabolism, disease, and drug response. But results published today (November 17) in PNAS reveal widespread differences between human and mouse gene expression, both in protein-coding and noncoding genes, suggesting that understanding these disparities could help explain fundamental differences in the two species’ physiology. Mice are widely used to model human metabolism, disease, and drug response. But results published today (November 17) in PNAS reveal widespread differences between human and mouse gene expression, both in protein-coding and noncoding genes, suggesting that understanding these disparities could help explain fundamental differences in the two species’ physiology. Michael Snyder of Stanford University and his colleagues compared how genes are expressed in 15 different human and mouse tissues, including brain, heart, liver, and kidney. They found that gene expression patterns clustered by species rather than tissues. For example, gene expression in a mouse liver more closely resembled the patterns observed in a mouse heart than those observed in a human liver. https://uncommondescent.com/genetics/mouse-gene-expression-reveals-widespread-differences-from-humans/ Our Microbes, Ourselves: Billions of Bacteria Within, Essential for Immune Function, Are Ours Alone - ScienceDaily (June 21, 2012) Excerpt: Chung repeated the experiment, only this time populating a third group of mice with microbes common to rats. This new group showed the same immune system deficiency as the humanized mice. "I was very surprised to see that," Chung said. "Naturally, I would have expected more of a half-way response." http://www.sciencedaily.com/releases/2012/06/120621130643.htm
This 'incompatibility' problem is widespread:
Animal Testing Is Bad Science: Point/Counterpoint Excerpt: The only reason people are under the misconception that animal experiments help humans is because the media, experimenters, universities and lobbying groups exaggerate the potential of animal experiments to lead to new cures and the role they have played in past medical advances.,,, The Food and Drug Administration (FDA) has noted that 92 percent of all drugs that are shown to be safe and effective in animal tests fail in human trials because they don’t work or are dangerous.,,, Physiological reactions to drugs vary enormously from species to species. Penicillin kills guinea pigs but is inactive in rabbits; aspirin kills cats and causes birth defects in rats, mice, guinea pigs, dogs, and monkeys; and morphine, a depressant in humans, stimulates goats, cats, and horses. http://www.peta.org/issues/animals-used-for-experimentation/animal-testing-bad-science.aspx
'Evolutionary reasoning' simply does not provide a fruitful heuristic in developing effective drugs to combat virulent diseases as many people have falsely been led to believe. In fact, IMHO, the most surefire way of developing effective drugs to combat virulent diseases is to realize that there are strict limits as to what evolutionary processes can be expected to accomplish. Dr. Behe puts the 'Intelligent reasoning' behind developing effective drugs like this:
Guide of the Perplexed: A Quick Reprise of The Edge of Evolution - Michael Behe - August 20, 2014 Excerpt: If there were a second drug with the efficacy of chloroquine which had always been administered in combination with it (but worked by a different mechanism), resistance to the combination would be expected to arise with a frequency in the neighborhood of 1 in 10^40 -- a medical triumph. http://www.evolutionnews.org/2014/08/guide_of_the_pe089161.html
The multiple drug cocktail that has been so effective in controlling HIV uses much the same strategy of being beyond the 'edge of evolution' that Dr. Behe has elucidated:
When taking any single drug, it is fairly likely that some mutant virus in the patient might happen to be resistant, survive the onslaught, and spawn a resistant lineage. But the probability that the patient hosts a mutant virus that happens to be resistant to several different drugs at the same time is much lower.,,, it "costs" a pest or pathogen to be resistant to a pesticide or drug. If you place resistant and non-resistant organisms in head-to-head competition in the absence of the pesticide or drug, the non-resistant organisms generally win.,,, This therapy has shown early, promising results — it may not eliminate HIV, but it could keep patients' virus loads low for a long time, slowing progression of the disease. http://evolution.berkeley.edu/evolibrary/article/medicine_04
Here is research of a promising new antibiotic that could singly, or perhaps in combination with other antibiotics, surpass Dr. Behe's 2 protein-protein binding site limit in MRSA:
New class of antibiotics discovered by chemists - March 7, 2014 Excerpt: Researchers who screened 1.2 million compounds found that the oxadiazole inhibits a penicillin-binding protein, PBP2a, and the biosynthesis of the cell wall that enables MRSA to resist other drugs. http://www.sciencedaily.com/releases/2014/03/140307165953.htm
Of related note: As to the somewhat minor extent 'evolutionary reasoning' has influenced medical diagnostics over the past several decades, it has led to much medical malpractice:
Evolution's "vestigial organ" argument debunked Excerpt: "The appendix, like the once 'vestigial' tonsils and adenoids, is a lymphoid organ (part of the body's immune system) which makes antibodies against infections in the digestive system. Believing it to be a useless evolutionary 'left over,' many surgeons once removed even the healthy appendix whenever they were in the abdominal cavity. Today, removal of a healthy appendix under most circumstances would be considered medical malpractice" (David Menton, Ph.D., "The Human Tail, and Other Tales of Evolution," St. Louis MetroVoice , January 1994, Vol. 4, No. 1). "Doctors once thought tonsils were simply useless evolutionary leftovers and took them out thinking that it could do no harm. Today there is considerable evidence that there are more troubles in the upper respiratory tract after tonsil removal than before, and doctors generally agree that simple enlargement of tonsils is hardly an indication for surgery" (J.D. Ratcliff, Your Body and How it Works, 1975, p. 137). The tailbone, properly known as the coccyx, is another supposed example of a vestigial structure that has been found to have a valuable function—especially regarding the ability to sit comfortably. Many people who have had this bone removed have great difficulty sitting. http://www.ucg.org/science/god-science-and-bible-evolutions-vestigial-organ-argument-debunked/
bornagain77_{May 18, 2015
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From the paper: Genomic DNA was purified from C. rodentium strain DBS100 with the Qiagen DNeasy kit no. 69504. The genome was se- quenced using the Illumina MiSeq sequencing system, which pro- duced 2.2-M random paired-end reads of 32 to 300 bases per read. After quality analysis with FastQC, reads were assembled using Spades (v 3.0), Velvet (v 1.1.06), and Bio Star, with standard pa- rameters for MiSeq data obtained from E. coli-like genomes. The highest quality genome assembly utilized for public database sub- mission was produced using Bio Star and contains 361 total con- tigs of 411 to 138,720 bp in length. The mean contig length is 14,919 bp, median contig length is 5,883 bp, and total assembly size is 5,385,810 bp (contig N50, 34,885). The submitted genome assembly was annotated using the NCBI Prokaryotic Genomes Annotation Pipeline (2.9, rev.456657). The annotation method utilized a best-placed reference protein set (GeneMarkS????). Identified features include 5,268 genes, 4,828 CDS, 305 pseudogenes, 1 clustered regularly inter- spaced short palindromic repeat (CRISPR) array, 38 rRNAs (5S, 16S, and 23S), 80 tRNAs, 17 noncoding RNAs (ncRNAs), and 103 frame-shifted genes. The cost of sequencing a genome has dropped to below $10,000 and you can purchase the machines and kits to do it on the open market. Even Liberty University can do it. Homework assignment: How much junk DNA did the Liberty boys discover?MatSpirit_{May 18, 2015
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LOL – competition between males explains the origin of males.
You might try reading the first sentence of the press release... The Citrobacter papers seems fine for what it is, but it's interesting to note how much evolutionary reasoning goes into the pipelines they used to do the annotation.wd400_{May 18, 2015
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awstar “Population benefits of sexual selection explain the existence of males” LOL - competition between males explains the origin of males. Good solid science there - unlike the creationists who are going to destroy Western civilization with their science-denial.Silver Asiatic_{May 18, 2015
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There is something very wrong with the referenced paper. There are no philosophical assertions, only scientific statements. To be real science there MUST be statements like the following: "Population benefits of sexual selection explain the existence of males" http://www.eurekalert.org/pub_releases/2015-05/uoea-pbo051515.phpawstar_{May 18, 2015
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Eh. Seems to be Citrobacter rodentium rather than E. coli, which was done in the 90s.daveS_{May 18, 2015
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goddiditMung_{May 18, 2015
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