Does Darwinian Evolution Explain Antibiotic Resistance?

_{William Dembski

February 7, 2006

Evolution, Intelligent Design}

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20 January 2006:
Vol. 311. no. 5759, pp. 374 – 377
SCIENCE

Sampling the Antibiotic Resistome
Vanessa M. D’Costa, Katherine M. McGrann, Donald W. Hughes, Gerard D. Wright

Microbial resistance to antibiotics currently spans all known classes of natural and synthetic compounds. It has not only hindered our treatment of infections but also dramatically reshaped drug discovery, yet its origins have not been systematically studied. Soil-dwelling bacteria produce and encounter a myriad of antibiotics, evolving corresponding sensing and evading strategies. They are a reservoir of resistance determinants that can be mobilized into the microbial community. Study of this reservoir could provide an early warning system for future clinically relevant antibiotic resistance mechanisms.

Comments

Joseph I am sayimg that there most certainly is destiny and no one controls it exactly as Einstein has maintained. We are all victims; some of us have been luckier than others.John Davison_{February 12, 2006
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Joseph: "Has anyone (besides moi) read Not By Chance by Dr. Lee Spetner?" I've read it and have it in my library. It's one of the better books I've read on evolution. His number crunching is very impressive. Given his credentials, the numbers he comes up with are very believeable--and I like his theory. Quite Lamrackian; but nice.PaV_{February 10, 2006
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I have also been banned at ARN but will accept what the data demonstrates. I also understand that (organic) evolution is what takes place after life appears- whatever that life may be.Joseph_{February 10, 2006
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I have been banned at ARN and I will never accept Special Creation. It is pure unadulterated fundamentalist mysticism and has no place in any serious discussion of organic evolution. As for explaining myself, you will find my publihsed views on the side board so there is no reason to repeat them here.John Davison_{February 10, 2006
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John Davison tells us: Nobody controls his destiny. You may write that down. Nobody also posts over on the ARN discussion board. :) But anyway- could you (JD) please clarify your post? Are you saying there isn't any "destiny" or that no one has control?Joseph_{February 9, 2006
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boseman asked scordova, Paul A. Nelson is a YEC who denies common descent. Do you agree with that position? Do you believe that animals with 2-chambered hearts were created seperately from those with 3-chambered hearts?
I think there is a good chance they were created seperately. An alternative is PEH, but my personal leanings are special creation. Leo Berg makes very good arguments regarding the difficulty of Darwinian intermediates, and that applies to the formation of radically different circulatory systems such as various hearts. I looked at a supposed intermediate of the 2-to-3 transition, namely, the lungfish. It's fair to say the lungfish heart only makes matters worse, not better for the Darwinian view. I you wish to classify me as something, classify me as a non-dogmatic YEC. That is, I sympahtize with it 80%, but am open to other possibilities. I was OEC 4 years ago until variable speed of light came on the table in 2002 in the journal Nature. The fossil record supports sudden emergence of fully formed creatures, with presumably fully formed hearts. Further, Salthe's corrolary to Fisher's fundamental theorem of Natrual Selection argues vital organs (like hearts) are the least likely organs to evolve via Natural Selection! Darwinism is in horrible shape empirically and theoretically, and it's baffling a theory is such sorry shape is so doggedly defended.scordova_{February 9, 2006
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Nobody controls his destiny. You may write that down.John Davison_{February 9, 2006
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Boesman, Any scientist worth their salt is open to whatever the data demonstrates. Is there ANY data that demonstrates a population of single-celled organisms can "evolve" into anything but a population of single-celled organisms? What happens once "science" determines what makes an organism what it is and we realize no amount of mutations can account for the range of differences? Chris Hyland tells us: Remember that it is not the bacteria that is mutating itself, but it is turning of its defence and allowing more frequent mutation, or removing a shield from in front of the target. You should remember THAT is what is being debated- does the cell (organism) control its destiny? At least some scientists seem to think it is so.Joseph_{February 9, 2006
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scordova, Paul A. Nelson is a YEC who denies common descent. Do you agree with that position? Do you believe that animals with 2-chambered hearts were created seperately from those with 3-chambered hearts?Boesman_{February 8, 2006
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I'm a creationist, but I don't argue Biblical Kinds to question common descent, nor do I argue NS as preserving a species to argue against common descent. I argue the difficulty of undirected macro-evolution to evolve things like a 2 chambered heart into a 3 chambered heart, or as Paul Nelson astutley observed, Problems with Characterizing the Protostome-Deuterostome Ancestor. In light of that, then one can make the inference of NS role in preserving a species. I don't use NS's role in preserving a species to a starting premise, it is a conclusion. Conclusions are not the same as premises.
...the stronger must always prevail over the weaker, the latter, in a state of nature, is allowed but few opportunities of continuing its race. In a large herd of cattle, the strongest bull drives from him all the younger and weaker individuals of his own sex, and remains sole master of the herd; so that all the young which are produced must have had their origin from one which possessed the maximum of power and physical strength; and which, consequently, in the struggle for existence, was the best able to maintain his ground, and defend himself from every enemy. -- Edward Blyth, 1835
http://www.bradburyac.mistral.co.uk/blyth1.html#strugglescordova_{February 8, 2006
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scordova, "Much credit of Natural SelectionÃ¢â‚¬â„¢s real role in biology should go to creationist Edward Blyth who saw itÃ¢â‚¬â„¢s proper role in preserving, not originating species." Do you agree with this? I ask because it sounds very much like an argument a creationist would use to deny common descent in favour of created "kinds".Boesman_{February 8, 2006
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Thank you for the kind words, Red Reader. :-)scordova_{February 8, 2006
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Salvador, Thank you for a fantastic education today!Red Reader_{February 8, 2006
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Well Chris, I think we're on good terms here, I appreciate your participation. I appreciate your open-minded approach and healthy skepticism. regards, Salvadorscordova_{February 8, 2006
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I agree that specific applications of systems biology, especailly to bioengineering, such as flux simulations, in their simplest form, do not require knowledge of the evolutionary processes, so may statement may have been rash. The major task of systems biology from a biologists perspective is to understand how the network arose in its current structure, and use this knowledge to study function of unknown network components, and to predict how the system may evolve, eg due to stress response. This means that whether or not evolution was a guided process does become important, a designed system will look different from an evolved system, and there is much work attempting to create artificail biological networks by mimicking evolutionary processes. Contrasting biological systems with designed systems has yeilded many insights in systems biology. It may be possible to investigate these systems from an intelligent design perspective, assuming that design was involved in their formation, but it has not been done as far as I am aware. I agree that using the term 'junk dna' to apply to all DNA that seems to have no function is a bad idea, although there is much research attempting to find functional non coding DNA.Chris Hyland_{February 8, 2006
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Little-known fact: Darwin himself believed in the transmission of aquired characteristics, what is now called "Lamarckian inheritance". He believed that natural selection acted upon such characteristics to increase their prevalance in the population. It was only with the coming of the "neo darwinian synthesis" in the West that "Larmarkianism" was banished. Interestingly, it was not banished on account of any great empirical refutation - there continues to be a good amount of evidence for the inheritance of acquired characteristics - but on theoretical grounds: if everything depends on genes, and the only way to change an organism is to mutate it's genome, then there is no mechanism by which acquired characteristics can be transmitted. Therefore, they aren't - QED.jimbo_{February 8, 2006
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Chris wrote: "This field completely depends on evolution being a non-guided process, and simulations of systems using this assumption perform pretty well. " I think that is grossly inaccurate. Systems biology will operate just fine when it agnostic to the issue of a biological origins,. Assuming it evolved from some pri-mordial goo via abiogenesis and Darwinian evolution adds nothing to the understanding of the system. Darwinism is a superflous add on that does nothing to extend scientific understanding. We don't have to assume an intelligence designed it, but we do have to assume the system has a design. Whether abiognesis plus Darwinism was the manufacturing mechanism is irrelevant to describing the funcitoning of the system, except for perhaps the fact it hinders the understanding of the system, because Darwinist are too quick to label something as useless or a bad design, rather than trying to understand the systems context of why something is there. For example, the emphasis and label of "junk DNA" has hindered progress in trying to frame the reason it exists from a system standpoint. There could be a breakthrough in understanding biology by studying "junk DNA" and uncovering it's purpose, but the attitude it's some collosal artifact of a blindwatchmaker is hindering scientific investigation.scordova_{February 8, 2006
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There was a paper out within the last year where they said they had "stopped" evolution in bacteria. Here's an article about it: http://www.the-scientist.com/article/display/15763/ And here's a quote from the article: "Floyd Romesberg, assistant professor of chemistry at Scripps Research Institute in San Diego, contends that evolution of new resistance genes can be stopped, or at least slowed by a factor of ten thousand." They tried to inhibit a particular pathway in the survival response of bacteria (I'm recalling this from memory), and were able to "stop" mutation. Thus, there is a "pathway" to this evolution response; and the response is random; but is the triggering of it, and the overall mechanism of it, random?PaV_{February 8, 2006
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Systems biology in no way assumes that natural biological systems were designed or engineered. It is simply a way of representing reactions between biological entites as data that lends is self to analysis by computational techniques designed for other networks. This field completely depends on evolution being a non-guided process, and simulations of systems using this assumption perform pretty well. What you say may be true, but it has yet to be proved as far as i am aware.Chris Hyland_{February 8, 2006
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Darwin gets too much credit for Natural Selection. He argued it as the origin of large scale biological innovation. Much credit of Natural Selection's real role in biology should go to creationist Edward Blyth who saw it's proper role in preserving, not originating species. Darwin gave Natural Selection a bad name. Shame on him.scordova_{February 8, 2006
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If I may offer at least a very modest interpretation: if we see statistically random (as in something like a guasian or other "random" distribution) phenomena in an adaptive response, we can not assume it was not designed. As I pointed out, it can not negate the design inference. Natural Selection and adaptation are unfortunately equivocated with Darwinism. Darwinism extrapolates these very true mechanisms as the origin of large scale biological innovation. What ends up happening is we take true statements (the existence of NS and adaptation) and say "therefore Darwinism is true". It is muddled reasoning. Chris wrote: "we have to assume this statistically random process undesigned until we have evidence to the contrary prediction of the evolutionary capability of microorganisms based on this assumption seems to work pretty well, prediction based on the opposite assumption do not.". I'm afraid this is what is hindering our understanding and it is an unhelpful approach to solving problems in biology. We already assume large scale design in biology (that's why the entire field of systems biology is emerging, view biology as an engineered entity). If we look at an organism that is pre-programmed to adapt through a genetic algorithm, we have a greater chance of defeating it. It's like figuring the heuristic of a chess program. If we approach the combatting of germs like we would try to combat a designed germ warfare attack, we might be a little more effective. I recommend this article which shows the other side of the adaptation war by my dear friend Royal Truman: http://www.trueorigin.org/b_cell_maturation.asp What it shows is that there is information warfare going on at the microbial level. To view the war of germs versus humans as some sort of "random noise vs. random noise" rather than "heuristic vs heuristic" will make our approach to the issues less scientifically effective. Darwinism is a superflous, unhelpful add-on that only muddles exploration rather than clarifies it. Salvadorscordova_{February 8, 2006
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Remember that it is not the bacteria that is mutating itself, but it is turning of its defence and allowing more frequent mutation, or removing a shield from in front of the target. I never meant to say that this is nonrandom, but the position on the genome of the mutations is, so far as the organsim does not direct the mutation. This is certainly not the only method of resistance, and mutations will still occur despite the DNA repair mechanism, but the affect on the organism of the mutations is no more or less random. We have to assume this statistically random process is undesigned until we have evidence to the contrary, prediction of the evolutionary capability of microorganisms based on this assumption seems to work pretty well, prediction based on the opposite assumption do not.Chris Hyland_{February 8, 2006
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A shot gun fires pellets in a pattern that is statistically described as random, but the random pattern is by design, it is part of a pre-determined search mechanism (so to speak) to hit a target. It is difficult then to say, just because the behavior of a system has some characteristics that are statistically random, that this implies no design. A modem signal has aspects that are statistically random, and that randomness is by design otherwise the bit rate would be sub-optimal!!! Natural Selection was well presented as a theory for preservation of species by creationist Edward Blythe prior to Darwin. That view is the correct perspective on seleciton's effect on biological entities. Selection (either natural or artificial) runs up against limits pretty quickly. All our population genetic models for real world verifiable examples presume the fundamental species will at most sub-speciate. Fruitflies will remain fruitflies. Massive biological innovation does not happen through RMNS, nor is it likely that it ever did. Darwinism claims credit for concepts it didn't invent and extrapolates valid ideas (like natural selection for the preservation of existing species) into un-warrented territory. The pro-Darwin crowd effectively presume that things that are statistically random are automatically undesigned. And as I pointed out, that is not necessarily true.scordova_{February 7, 2006
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Certain bacteria do have what is called antigenic variation, which is comparable to the immune system, however this is not the usual case, and the evolution of this system has been well studied. The main forms of resistance are: Horizontal gene transfer of genes that confer resistance from other bacteria, and random mutations. Mutations which confer resistance usually alter the sequence of proteins that are drug targets, causing the drug to no longer be able to bind to the target protein that still retains its function. I imagine this could also be acheived by gene duplication. These mutations are what occur when bacteria increase their rate of mutation. This is still a random process, in the sense that the bacteria is 'aware' of a problem due to stress, but does not know which specific mutations will solve the problem.
If I use a shotgun with buckshot at a skeet range I don't know which bit of shot, if any, will hit the target but it's still not a random shot. If I use a rifle I probably won't hit the target at all. It's not random if there's a targeted response. The bacteria are actively responding. Their response is no more random than the buckshot.-ds Chris Hyland_{February 7, 2006
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Thanks DaveScot. But this also illustrates a problem. OldCola asks: Joseph, introns? In bacteria? Are you serious? All that had to be done was (as DaveScot did) for OldCola to go to google and type in "introns in bacteria" (leaving out the "Joseph" and "are you serious?") and the answer would be given: introns in bacteria The problem it illustrates is that as opposed to doing very little basic research someone would rather try to question what I posted in a condescending manner. Sadly typical. It's too bad "dope slaps" can't be handed out over the ineternet... :)Joseph_{February 7, 2006
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Dr. Michael Behe in "Darwin's Black Box" writes about how the number of antibodies the body can produce is hugely increased by "mixing and matching DNA segments". It seems to me that a similar system could exist in bacteria to counter toxins. If so, then random mutation has nothing to do with it; the bacteria is actively going through a "toolkit" of pre-designed possible antidotes. If there is any randomness it might be similar to reaching into a bag and extracting the solutions at random. The extraction, however, has not created anything fundamentally new, it has merely selected, at random from one of the huge number of pre-existing possibilities. Rather than an argument from random mutation and natural selection, the system could be yet another intelligently designed, irreducibly complex system. Those bacteria that die are the ones not lucky enough to extract the correct tool from the bag of tricks. I guess you could call that part natural selection.SCheesman_{February 7, 2006
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What exactly is the difference between Lamarkian and Darwinian inheritance in single celled organisms? It has been known for some time that bacteria are able to increase their rate of mutation in response to stress by altering their DNA repair mechanisms, however this just means an increase of random mutations.Chris Hyland_{February 7, 2006
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DaveScot

Lamarkian inheritance would be anathema to darwinism. I would be very interested in any primary source you could offer on such a phenomenon. I.e. that an individual bacterium is able to modify its own genome in a non-random way, rather than the appropriate mutation occurring by chance and being selected for by the ability to survive in the relevant environment. Demonstrating Lamarkian inheritance would be a remarkable development.

http://en.wikipedia.org/wiki/Lamarckism#Lamarckism_and_single_celled_organisms -ds
Xavier_{February 7, 2006
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That bacteria, when stressed, may react by "destabilising" their DNA repair system so that mutations arise more rapidly, does not seem to undermine my point, unless I am mistaken.

You were mistaken.
Absolutely not. They die. If one bacterium has mutated into a resistant form, it is then able to reproduce to fill the void left by its unresistant siblings. Natural selection favours survivors.

They don't all die. Are you familiar with the term LD 50 used in toxicity descriptions? It means Lethal Dose for 50% of the sample group. Not everything dies when being poisoned. Not all bacteria die when poisoned. Some of the them survive and the survivors turn on chemical defense cascades that actively modify genes that will be inherited. This is a Lamarckian mechanism - inheritance of acquired characters. Random mutation on the other hand depends on sheer luck for the background mutation rate to hit the right gene in the right way. Bacteria don't wait around for random mutation to supply the variation. -ds
Xavier_{February 7, 2006
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Xavier - you've obviously failed to read the Scripps article before responding.DaveScot_{February 7, 2006
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