Antibiotic resistance genes are everywhere now?

_{Denyse O'Leary

May 10, 2014

horizontal gene transfer, News}

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There is a very good reason microbes would be armed with antibiotic resistance genes, the researchers explain. After all, most antibiotics used in medicine are isolated from soil microorganisms, such as bacteria or fungi, in the first place. That means that the resistance genes were available long before humans put antibiotic drugs into use. Bacteria lacking them to start with can simply borrow them (via horizontal transfer of genes) from those that are better equipped.

Nesme and Simonet say the new findings should come as a plea for a broader ecological perspective on the antibiotic resistance problem.

“It is only with more knowledge on antibiotic resistance dissemination — from the environment to pathogens in the clinic and leading to antibiotic treatment failure rates — that we will be able to produce more sustainable antibiotic drugs,” Nesme says.

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Acartia_bogart: First of all, antibiotic resistance is a complex trait in most cases. Penicillinase, for example, is a complex protein (250 - 300 AAs). Only a few forms of resistance are due to simple mutations. My discussion is always about molecular functions. Proteins are functional only when they are functional. What is the adaptive value of ATP synthase, if it cannot perform ATP synthesis by a proton gradient? And, as I have clearly shown in recent posts, ATP synthase is a very old protein, which was already as it is now before the bacteria - archaea divergence. So, no need to ask any legally blind person. It's enough to know and understand biology and biochemistry.gpuccio_{May 12, 2014
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Gpuccio: You are assuming that antibiotic resistance is a complex trait, which it isn't. But the ID argument requires that complex traits (organs, morphology, proteins) must arise fully formed to be of any adaptive value. This simply isn't true. If you doubt that, ask any legally blind person if they would prefer to have no vision at all.Acartia_bogart_{May 12, 2014
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Acartia_bogart: It is contradictory to unguided evolution of complex traits. If NS only redistributes old traits that already existed, there is no real evolution in that. The simple fact is: in observed cases, complex traits have always been found to be "already existing", and there is no explanation of how they were first generated. See also the interesting examples of Lenski's experiment, and of the wrong interpretation of nylonase origin by Ohno. Simple traits (1-2 AAs) instead can well appear by RV, and be selected, in the rare contexts called usually "microevolution". Again, that does not help to explain the origin of complex traits. NS exists, but it has no role in the origin of complex traits. It's as simple as that.gpuccio_{May 11, 2014
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How is this contradictory to natural selection. Natural selection acts on traits expressed by genes. If organisms with a specific trait are better at reproducing than those without, that trait will become more and more prevalent. Whether the trait already existed, or whether it arose recently through mutation. Makes no difference. Antibiotic resistance in the absence of antibiotics would be of little value other than in local environments where the antibiotic occurs naturally. What has changed with medicine is the "environment" in which the bacteria live. Welcome to the world of natural selection.Acartia_bogart_{May 11, 2014
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Horizontal gene transfer seems to be common among bacteria, but bacteria seem to be a special category of organisms. Do dinosaurs have the advantage of horizontal gene transfer when trying to evolve into birds? I don't think so. They had to evolve all the new genes and software themselves without the aid of gene transfer. Horizontal gene transfer might help explain bacterial evolution, but it doesn't answer the question of where those genes came from to begin with. If one bacteria is lacking the gene, why not just evolve it yourself instead of being lazy and hoping to get a gift from a neighbor?!tjguy_{May 11, 2014
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BA: It can be worthwhile to remember that antibiotic resistance is of many different kinds. In most cases, it depends on complex and old proteins (like penicillinases which "evolved" 1-2 billion years ago, when antibiotics were not exactly available) and on HGT or similar mechanisms. Only a few cases can be intepreted as new mutations (usually 1 AA, exceptionally 2), and therefore viewed as cases of "microevolution" in a darwinian context.gpuccio_{May 11, 2014
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Needless to say that finding is not conducive to Darwinian thought. Then there was the MRSA scare, i.e. bacteria becoming resistant to multiple antibiotics, in which it is found that the cure for MRSA was to 'get a little dirty':
Are You Too Clean? - New Studies Suggest Getting A Little Dirty May Be Just What The Doctor Ordered - December 2010 http://www.creationsafaris.com/crev201012.htm#20101208a Superbugs not super after all Excerpt: It is precisely because the mutations which give rise to resistance are in some form or another defects, that so-called supergerms are not really ‘super’ at all—they are actually rather ‘wimpy’ compared to their close cousins. http://creation.com/superbugs-not-super-after-all French Volcanic Clay Kills Antibiotic-Resistant MRSA Superbug Excerpt: I've heard of some people being told to "go roll around in the dirt" to get rid of their MRSA, and I've heard some reports of that working. I believe the effect was in "normalizing" their resident bacteria living on their skin. Just like in our digestive system, bacteria live in balance. Put more of the "good" guys in, and that will support your body being in balance. http://staph-infection-resources.blogspot.com/2008/04/french-volcanic-clay-kills-antibiotic.html MRSA - Supergerms Do they prove evolution? In places that are exposed to dirt from the street—such as your house—the supergerms are kept in their place not by powerful drugs and poisons but by competition with other germs. And their resistance genes are diluted by genes of the susceptible or non-resistant germs of the same species rather than being concentrated by selective breeding. That is why most non-hospital infections respond readily to antibiotics—the drug kills most of the germs, the body takes care of the rest. If it were not so, the so called supergerms would escape from hospitals and sweep the world. http://www.answersingenesis.org/creation/v11/i2/supergerms.asp
Of related note to developing a 'resistance proof' antibiotic medicine that is beyond Dr. Behe's 'Edge of Evolution' (2 protein-protein binding site limit), i.e. a medicine that even MRSA will have trouble overcoming, the following study was interesting:
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 "The likelihood of developing two binding sites in a protein complex would be the square of the probability of developing one: a double CCC (chloroquine complexity cluster), 10^20 times 10^20, which is 10^40. There have likely been fewer than 10^40 cells in the entire world in the past 4 billion years, so the odds are against a single event of this variety (just 2 binding sites being generated by accident) in the history of life. It is biologically unreasonable." Michael J. Behe PhD. (from page 146 of his book "Edge of Evolution")
Of related note at how antithetical Darwinian thought is in all this:
Richard Dawkins interview with a 'Darwinian' physician goes off track - video Excerpt: "I am amazed, Richard, that what we call metazoans, multi-celled organisms, have actually been able to evolve, and the reason [for amazement] is that bacteria and viruses replicate so quickly -- a few hours sometimes, they can reproduce themselves -- that they can evolve very, very quickly. And we're stuck with twenty years at least between generations. How is it that we resist infection when they can evolve so quickly to find ways around our defenses?" http://www.evolutionnews.org/2012/07/video_to_dawkin062031.html
i.e. Since successful reproduction is all that really matters on a neo-Darwinian view of things, how can anything but successful reproduction be realistically 'selected' for? Any other function besides reproduction, such as sight, hearing, thinking, etc.., would be highly superfluous to the primary criteria of successfully reproducing, and should, on a Darwinian view, be discarded as so much excess baggage since it would slow down successful reproduction. But that is not what we find. The following researchers recently were 'surprised' by what they found:
Doubting Darwin: Algae Findings Surprise Scientists - April 28, 2014 Excerpt: One of Charles Darwin's hypotheses posits that closely related species will compete for food and other resources more strongly with one another than with distant relatives, because they occupy similar ecological niches. Most biologists long have accepted this to be true. Thus, three researchers were more than a little shaken to find that their experiments on fresh water green algae failed to support Darwin's theory — at least in one case. One of Charles Darwin's hypotheses posits that closely related species will compete for food and other resources more strongly with one another than with distant relatives, because they occupy similar ecological niches. Most biologists long have accepted this to be true. Thus, three researchers were more than a little shaken to find that their experiments on fresh water green algae failed to support Darwin's theory — at least in one case. "It was completely unexpected," says Bradley Cardinale, associate professor in the University of Michigan's school of natural resources & environment. "When we saw the results, we said 'this can't be."' We sat there banging our heads against the wall. Darwin's hypothesis has been with us for so long, how can it not be right?" The researchers ,,,— were so uncomfortable with their results that they spent the next several months trying to disprove their own work. But the research held up.,,, The scientists did not set out to disprove Darwin, but, in fact, to learn more about the genetic and ecological uniqueness of fresh water green algae so they could provide conservationists with useful data for decision-making. "We went into it assuming Darwin to be right, and expecting to come up with some real numbers for conservationists," Cardinale says. "When we started coming up with numbers that showed he wasn't right, we were completely baffled.",,, Darwin "was obsessed with competition," Cardinale says. "He assumed the whole world was composed of species competing with each other, but we found that one-third of the species of algae we studied actually like each other. They don't grow as well unless you put them with another species. It may be that nature has a heck of a lot more mutualisms than we ever expected. "Maybe species are co-evolving," he adds. "Maybe they are evolving together so they are more productive as a team than they are individually. We found that more than one-third of the time, that they like to be together. Maybe Darwin's presumption that the world may be dominated by competition is wrong." http://www.livescience.com/45205-data-dont-back-up-darwin-in-algae-study-nsf-bts.html
Indeed, instead of eating us, time after time these different types of microbial life are found to be helping us in essential ways that have nothing to do with the primary criteria of successfully reproducing,,,
NIH Human Microbiome Project defines normal bacterial makeup of the body – June 13, 2012 Excerpt: Microbes inhabit just about every part of the human body, living on the skin, in the gut, and up the nose. Sometimes they cause sickness, but most of the time, microorganisms live in harmony with their human hosts, providing vital functions essential for human survival. http://www.nih.gov/news/health/jun2012/nhgri-13.htm
In other words:
The Microbial Engines That Drive Earth’s Biogeochemical Cycles - Falkowski 2008 Excerpt: Microbial life can easily live without us; we, however, cannot survive without the global catalysis and environmental transformations it provides. - Paul G. Falkowski - Professor Geological Sciences - Rutgers http://www.genetics.iastate.edu/delong1.pdf
bornagain77_{May 11, 2014
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I remember when antibiotic resistance was cited fairly often by Darwinists on UD as supposed 'proof' of evolution. And it would always be pointed out to them that,,,
List Of Degraded Molecular Abilities Of Antibiotic Resistant Bacteria: http://www.trueorigin.org/bacteria01.asp Helping an Internet Debater Defend Intelligent Design - Casey Luskin - May 3, 2014 Excerpt: antibiotic resistance entails very small-scale degrees of biological change.,,, antibiotic resistant bacteria tend to "revert" to their prior forms after the antibacterial drug is removed. This is due to a "fitness cost," which suggests that mutations that allow antibiotic resistance are breaking down the normal, efficient operations of a bacterial cell, and are less "advantageous. http://www.evolutionnews.org/2014/05/helping_an_inte085171.html Is Antibiotic Resistance evidence for evolution? - 'The Fitness Test' - video https://www.youtube.com/watch?v=rYaU4moNEBU Thank Goodness the NCSE Is Wrong: Fitness Costs Are Important to Evolutionary Microbiology Excerpt: it (an antibiotic resistant bacterium) reproduces slower than it did before it was changed. This effect is widely recognized, and is called the fitness cost of antibiotic resistance. It is the existence of these costs and other examples of the limits of evolution that call into question the neo-Darwinian story of macroevolution. http://www.evolutionnews.org/2010/03/thank_goodness_the_ncse_is_wro.html
etc.. etc.. But the claims from Darwinists, at least here on UD, that antibiotic resistance is 'proof' of Darwinian evolution now seem to have dried up once it was discovered that antibiotic resistance is ancient:
A Tale of Two Falsifications of Evolution - September 2011 Excerpt: “Scientists were surprised at how fast bacteria developed resistance to the miracle antibiotic drugs when they were developed less than a century ago. Now scientists at McMaster University have found that resistance has been around for at least 30,000 years.” http://crev.info/content/110904-a_tale_of_two_falsifications_of_evolution (Ancient) Cave bacteria resistant to antibiotics - April 2012 Excerpt: Antibiotic-resistant bacteria cut off from the outside world for more than four million years have been found in a deep cave. The discovery is surprising because drug resistance is widely believed to be the result of too much treatment.,,, “Our study shows that antibiotic resistance is hard-wired into bacteria. It could be billions of years old, but we have only been trying to understand it for the last 70 years,” said Dr Gerry Wright, from McMaster University in Canada, who has analysed the microbes. http://www.scotsman.com/news/health/cave-bacteria-resistant-to-antibiotics-1-2229183# 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 Vreeland was a lot less cooperative when I asked him about a fitness test on the 250 million year old bacteria, saying 'only a creationist would ask such a question', but Dr. Cano who worked on 30 million year old bacteria stated in reply to a personal e-mail from myself, "We performed such a (fitness) 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.": RJ Cano and MK Borucki Fitness test which compared ancient bacteria to its modern day descendants,
bornagain77_{May 11, 2014
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