“There is no controversy”

_{William Dembski

May 22, 2008

Evolution}

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“There is no controversy.” “There should be no controversy.” “It’s okay to expel those who pretend that there is a controversy.” “Academic freedom does not apply where the scientific consensus says there is no controversy.” …

The Washington Post has a ridiculous editorial that elevates evolutionary theory to the same status as gravitational theory and the truths of mathematics (go here).

Meanwhile, the Altenberg meeting coming up this summer brings together biologists who see the contemporary state of evolutionary theory as in upheaval (go here). Yes, the field is in disarray, but there is NO CONTROVERSY. What, are we living in a Kafka novel?

Comments

Dr. Cano wrote me back to say he doesn't have an opinion one way or the other as far as gaining or losing complexity. So I asked (begged) him for more detailed information so the guys around here could do a detailed analysis of the differences. (Because of EXPELLED) I assured him that his personal opinion will be stated clearly. In which his stated opinion is firmly undecided as to whether it has gained or lost complexity.bornagain77_{June 2, 2008
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bornagain77: Well, Cano's answer seems to point to some narrowing of function, as you say, but still it is too vague. It would be interesting to know wxactly what the observed differences, and if they could be ascribed to some difference in the proteomes and in the genomes, and if those differences can be intepreted in evolutionary context. In other words, a lot of difficult work. In scientific research, after all, all amounts to available resources...gpuccio_{June 2, 2008
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gpuccio, this is what Dr. Cano wrote back in regards to comparing ancient and modern bacteria; 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. No antimicrobial panel was used. This is all the data we have and if you want specifics I'll have to dig through my old notebooks. But it's there somewhere. Gpuccio, correct me if I'm wrong but this shows a "narrowing" of flexibility for the modern bacteria thus conforming to genetic entropy. I wrote him back asking for more specifics. Well, what do you think gpuccio?bornagain77_{June 2, 2008
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a little more on Cano, Over the past few years, Cano and his team have claimed to have revived a whole range of microorganisms from dormant spores trapped in amber (New Scientist, Science, 27 May 1995, p 18). Most of the microorganisms have been very similar to living examples, but their latest bacterium is quite unlike modern species of Staphylococcus. Cano says that the bacteria are very unusual, often multiplying to form clusters that resemble a ship's wheel. And whereas the cell walls of today's Staphylococcus are rich in the amino acid L-lysine, this substance is not found in S. succinus. Instead, their cell walls are laden with diaminopimelic acids and a fatty acid called tuberculostearic acid, which are found in the walls of modern Corynebacterium. "It's like science fiction, but it's cool," says Cano, who is submitting his findings for publication to the International Journal of Systematic Bacteriology. http://www.newscientist.com/article/mg15420821.100-amber-alien-surprises-lazarus-team.htmlbornagain77_{June 2, 2008
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gpuccio, In Digging a little deeper to Cano's work I found this. http://query.nytimes.com/gst/fullpage.html?res=990CEFD61439F93AA25756C0A963958260&sec=&spon=&pagewanted=2 excerpt: Dr. Cano said that most of the ancient microorganisms he had cultured were strains of Bacillus sphaericus, a harmless bacterium common today in soil and in the bodies of insects. Whether or not the strains of Bacillus sphaericus found in amber are essentially identical to modern bacteria remains to be seen; skeptics who contend that they are the same say that this shows the "ancient" bacteria to be nothing more than modern contamination. But Dr. Cano and his former graduate student Dr. Monica K. Borucki said that they had found slight but significant differences between the DNA of the ancient, amber-sealed Bacillus sphaericus and that of its modern counterpart. The small genetic differences could be explained as the result of evolutionary change over 30 million years, during which modern Bacillus sphaericus diverged from its ancient form, he said. Skeptics point out, however, that the slight genetic difference might also be explained in terms of normal variation between individual bacteria. Biologists are likely to argue over this point for some time. ---- Thus gpuccio, it appears that Cano's work lines up with Vreeland's as well as the revival of the apparent extinct species by Helga Stan-Lotter, makes the case airtight imo that these are indeed ancient. Thus all lines for genetic entropy/conservation of information, that may be able to be drawn from here on out will stand against criticism.bornagain77_{June 2, 2008
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gpuccio, I believe another criticism leveled against Vreeland is that his work in reviving ancient bacteria was not duplicated, yet here is a study that seems to duplicate his findings in reviving ancient bacteria although the species appears to be novel with no decendent species: http://mic.sgmjournals.org/cgi/content/full/145/12/3565 Very similar strains of Halococcus salifodinae are found in geographically separated Permo-Triassic salt deposits Helga Stan-Lotter1, Terry J. McGenity2, Andrea Legat1, Ewald B. M. Denner3, Kurt Glaser1, Karl O. Stetter4 and Gerhar Wanner5 Abstract: The authors have previously isolated a novel extremely halophilic archaeon, Halococcus salifodinae BIp, from Austrian rock salt deposited about 250 million years ago. In this study they compared strain BIp with two other halococci isolated independently from geographically distant salt deposits of similar age, and with two recent isolates (N1 and H2) from the same site as strain Blp. Strain BG2/2 was from a salt mine in Germany and strain Br3 from a halite deposit in England; both resembled Hc. salifodinae BIp in cellular and colonial morphology. Strains BIp, BG2/2 and Br3 had identical 16S rRNA sequences, very similar whole-cell protein patterns, which were different from those of other halococci, similar G+C contents and identical sequences in a 108-base insertion in their 5S rRNA gene. Other similarities included composition and relative abundances of polar lipids, antibiotic susceptibility, enzymic activities and Fourier-transform infrared spectra. Strains N1 and H2 showed similar morphology, whole-cell protein patterns and biochemical characteristics as strains BIp, Br3 and BG2/2. Their partial 16S rRNA sequences (682 and 641 bases, respectively) were indistinguishable from those of strains BIp, Br3 and BG2/2. Therefore strains N1 and H2 can be considered as reisolates of Hc. salifodinae which were obtained 8 years after the first samples were taken from that mine. The results presented suggest that viable halophilic archaea, which belong to the same species, occur in widely separated evaporite locations of similar geological age, and support the notion that these halophilic isolates from subterranean salt deposits may be the remnants of populations which inhabited ancient hypersaline seas.bornagain77_{June 2, 2008
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gpuccio, Here is a little more background on Vreeland's work: Row over ancient bacteria http://news.bbc.co.uk/2/hi/science/nature/1375505.stm Also here is a science blog that goes into some detail and is very informative on the matter: http://www.evcforum.net/cgi-bin/dm.cgi?action=msg&f=3&t=109&m=1 excerpt from blog; Modulous, you are correct to see the discovery of ancient bacteria DNA as problematic for mainstream evo assumptions, but the evo solution is basically just to deny the evidence, and that's frankly why I have a real problem with evolutionism. Evos start with ToE as the primary fact and then use that to argue whether data is correct or not, and then claim because all the data they accept agrees with ToE, that the theory is substantiated. It's circular reasoning. Let's look at the research on this finding since. The report elicited strong skepticism from many quarters. Biological chemists doubted that nucleic acids could remain pristine over such time periods. Even had the bacterium hibernated as a hardy spore, its DNA surely would have broken down over 250,000 millennia, if not from the barrage of ultraviolet light during its long-ago residence on the surface, then from naturally occurring terrestrial radiation over the Earth's evolution. Geologists questioned the age of the fluid inclusions, arguing that certain features of the Salado Formation (the source of the halite crystal) suggested that flaws in the rock had permitted the intrusion of more recent fluid (which, by inference, had carried more recent bacteria into the ancient rock). Geneticists pointed out that one of the bellwether genes that the group had sequenced—one that encodes the so-called 16S ribosomal subunit—was far too similar to its counterpart in another strain of bacteria. According to this critique, either the "ancient" bacterium was actually a contaminant, or its descendants had inexplicably failed to change in the past 250 million years. Yet Vreeland and an expanding circle of collaborators have followed up the original report with publications that seek to counter each of these criticisms. In 2002, he and two West Chester University colleagues reported in the International Journal of Radiation Biology their calculation that the degree of genetic damage caused by normal traces of radioactive potassium-40 in the surrounding rock was not great enough to rule out a quarter-billion years of bacterial survival. Scratch objection number 1. In April of 2005, the three authors from the Nature paper teamed with Tim K. Lowenstein, a geologist at Binghamton University in New York, and his student, Cindy L. Satterfield, in publishing a detailed report in the journal Geology. To test the idea put forth by critics that inclusions in the salt crystals were newer than the surrounding rock, they measured the temperature of original crystallization for samples from the same part of the Salado Formation that yielded Virgibacillus sp. 2-9-3. The team reasoned that if microbe-carrying fluid had recently reached the deeply buried salt deposit and recrystallized, the temperatures of those crystallizations would be similar. Instead, they found the opposite: The results ranged from 17 to 37 degrees Celsius, or about 63 to 99 degrees Fahrenheit, a distribution that suggests seasonal climatic variation. In other words, the crystals that formed around pockets of fluid (and presumably bacteria) were created on or near the surface instead of far underground. A second, more definitive, line of investigation examined the concentrations of various ions in the fluid inclusions. The balance of ions in seawater changes over geological time, so measuring them can provide an approximate date at which the saltwater crystallized. The ion concentrations in the halite inclusions matched those of oceans in the Permian period—a profile that is distinct from the seawater of today and also from larger pockets of trapped brine elsewhere in the Salado. As a final test, the team plans to use an ultrasensitive mass spectrometer to date tiny, individual inclusions by the rubidium-strontium method (87Rb decays into 87Sr with a half-life of 49 billion years). Scratch objection number 2. The third criticism, based on DNA similarities, has been harder to dismiss. Despite a protocol of sterilization and controls that even critics describe as "heroic," contamination remained a potential source of the 2-9-3 bacterium based on its molecular resemblance to current strains. Understandably, Vreeland defends the work against charges of contamination. He even views the genetic objections as the least valid, stating that of all the challenges (geologic, chemical and genetic), "this is by far the weakest of the critiques." http://www.americanscientist.org/template/AssetDetail/assetid/47368 All of the criticisms have been met with the sole exception that this cannot be ancient DNA because it's so similar to younger bacteria DNA that this doesn't fit with evo theories on the molecular clock, but is this an acceptable argument? No. It's like saying, hey, we know theory A is true, and so any fact that disagrees with theory A must be false, and so this piece of data is false. It's not real science, imo. Heck, even the critics of Vreeland state the tactics used to prevent contanimation are "herioc",but that doesn't really matter. They will argue any fact that disagrees with them must be the result of contanimation or some other issue, unless perhaps Vreeland can find a way to say the data really doesn't conflict, and then all the evos will say, hey, this is a good find or some such. Some more evidence: April 11, 2005 — A new study has confirmed that the brine and salt crystals in which scientists found a controversial 250-million-year-old bacteria truly form a quarter-billion-year time capsule. http://dsc.discovery.com/news/briefs/20050411/oldestlife.html http://news.bbc.co.uk/2/hi/science/nature/1375505.stm Edited by randman, 08-14-2006 09:16 PM: No reason given.bornagain77_{June 2, 2008
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Thanks gpuccio, Looks like the draft may be getting closer, (save for my grammer mistakes) and although I have hardly a clue for proper wording in this particular field of study(LOL). As well, I was thinking another avenue of inquiry may be in the amber bacteria that were revived. The scientist conducting the research (Cano) seems to be further along in his venture in some avenues, and it seems very likely he may have already done this type of testing. (At least that's the impression I get when i read he has developed "new antibiotics".) I haven't dug too deeply into Cano's work but this is what I found so far on his work on 25 to 40 million year old amber: Cano claims he resurrected at least 30 to 40 species of bacteria from ancient spores, and grew them on culture plates. Now he's analyzing those bacteria. Most, he says, are members of the genus Bacillus, an ancient, spore-forming group of bacteria that is widely distributed today. Some members of the genus (Bacillus thuringiensis) are used for biological control of insects. as well as this Revival and identification of bacterial spores in 25- to 40-million-year-old Dominican amber. Cano RJ, Borucki MK Science 1995 May 19;268(5213):1060-4 Published erratum appears in Science 1995 Jun 2;268(5215):1265 Biological Sciences, California Polytechnic State University, San Luis Obispo 93407, USA. A bacterial spore was revived, cultured, and identified from the abdominal contents of extinct bees preserved for 25 to 40 million years in buried Dominican amber. Rigorous surface decontamination of the amber and aseptic procedures were used during the recovery of the bacterium. Several lines of evidence indicated that the isolated bacterium was of ancient origin and not an extant contaminant. The characteristic enzymatic, biochemical, and 16S ribosomal DNA profiles indicated that the ancient bacterium is most closely related to extant Bacillus sphaericus. As well, gpuccio, it seems that ancient bacteria coming from ancient amber will take away many of the criticisms that Vreeland has had to overcome in his work and thus give the results for any Genetic Entropy that may be found in ancient bacteria comparisons of Vreeland's work much more traction, to all lines of ancient bacterial evidence that may be gathered. And if I recall correctly, the differences he found were similar to Vreeland's, that is to say that the molecular differences are far enough apart to rule out modern contaminants yet close enough to rule out evolution during that time. I firmly believe that this pending evidence could be a minor treasure trove for ID.bornagain77_{June 1, 2008
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bornagain77: As I promised, I have tried to re-write you text in a way which could be more technically detailed. Here it is: Dr. Vreeland, In looking through your studies on the suspected 250 million year old bacteria, I noticed that you showed that, although the "ancient" strain is very similar to the modern counterpart, there are several differences at the molecular level ehich can suggest that the bacteria were indeed different than modern strains, and that the suspected 250 million year old bacteria were indeed not modern contaminants. I was very impressed with your work and for what its worth I commend you on you on your excellent practice of science. Yet, a friend and I, in our brief looking at your paper (Fatty acid and DNA analyses of Permian bacteria) jusct wondered if it could be possible to campare the ancient starin with the modern one in a “fitness test", to show if the differences bewteen the two strains could imply a funcional difference in fitness. The simplest way to do that, in our opinion, could be to have the two strains co-cultured in standard conditions, or in any culture condition which may appear appropriate to test specific fitness issues, and see if one of the two strains shows a fitness advantage. The rationale for that is that, if we assume that the ancirnt strain is in some way a putative "ancestor" for the modern one, it would be interesting to understand if any fitness difference can be observed between the two strains in controlled laboratory conditions. That would be perinent in any evolutionary reasoning about this really interesting case, where we could be in the lucky position of being able to directly compare an ancient ancestor and its supposed modern descendant from a functional point of view. With Respect, Phil C.gpuccio_{June 1, 2008
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A little off topic: What are probiotics? http://health.yahoo.com/digestive-treatment/probiotics/healthwise--tw2302spec.html they suggest the preceding line of defence to combat "superbugs here: Gut superbug causing more illnesses, deaths http://health.yahoo.com/news/ap/deadly_bacteria.html Thus the "fitness cost" test is, in an auxillary fashion, actually effectively being used to bring the "superbugs" into check. But instead of the test tube, the human gut is where the "beneficial" bacteria are reintroduced to outcompete the mutated bacteria into oblivion.bornagain77_{May 29, 2008
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Bob O'H, As gpuccio noted, he thinks the test will show no difference in (reproductive) fitness , whereas I think the ancient will show a more robust (reproductive fitness in both ancient and modern environments, so if you don't mind me asking what do you think such a test will show for each environment.bornagain77_{May 29, 2008
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Bob O'H Thanks for your input. I was lokking for test in "most likely" ancient environment as well as test in modern environment, for I have a strong hunch that the ancient will actually perform better in both enviroments since the descendent strains have most likely been through several "hostile" environments in 250 million years, Environments that have degraded their genetic information in a sequential manner to where they will show a consistent loss of fitness no matter which environment (modern or ancient) they are compared to the parent strain in. Thanks for your input and as gpuccio stated we would appreciate any further input that would help insure we get a positive reponse.bornagain77_{May 29, 2008
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Bob O'H: I agree with your comments at #227. I think bornagain77 is thinking of just a simple co-culture in standard conditions, as is shown in the video he linked, where antibiotic resistant bacteria succunb to their "normal" counterpart when cultured again in normal conditions. Do you thimk that could be a reasonable test? Personally, I don't think it could detect any different fitness in this case, but who knows? As I am going to write a revised version of the question for bornagain, I would appreciate your input.gpuccio_{May 29, 2008
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Yet, a friend and I, in our brief looked at your paper (Fatty acid and DNA analyses of Permian bacteria) could not find a “fitness cost” test. The test which is commonly preformed on antibiotic resistant bacteria to find if a robust level of complexity has evolved. I was wondering if you have done such a measure for “fitness cost” between the suspected 250 Ma bacteria and any or all of its suspected decendent strains.
As a professional, I can tell you that by this point the recipient of the letter will have decided that you don't know what you're talking about. You would do better by asking whether they had compared the fitness of the ancient strain to modern bacteria. It might be good to be clear about what environment you think it should be tested in - obviously testing in a wrong environment will give useless results. The other problem with comparing fitnesses is evolution might have been more determined by Red Queen processes, so the fitness in the natal environment may not have changed, but the environment might have changed.Bob O'H_{May 28, 2008
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bornagain77: OK, I'll work on it and post here my version. Stay tuned.gpuccio_{May 28, 2008
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gpuccio, Here is the very rough draft. Please feel free to correct it in any measure necessary. Dr. Vreeland, In looking through your studies on the suspected 250 million year old bacteria, I noticed that you used several test at the molecular level to prove that the bacteria were indeed different than modern strains, and that the suspected 250 million year old bacteria were indeed not modern contaminants. I was very impressed with your work and for what its worth I commend you on you on your excellent practice of science. Yet, a friend and I, in our brief looked at your paper (Fatty acid and DNA analyses of Permian bacteria) could not find a "fitness cost" test. The test which is commonly preformed on antibiotic resistant bacteria to find if a robust level of complexity has evolved. I was wondering if you have done such a measure for "fitness cost" between the suspected 250 Ma bacteria and any or all of its suspected decendent strains. We are debating whether if any of the strains will display evolution, whether any of them will stay the same, or whether any of them regressed in regards to the parent strain (tested in both the suspected ancient "hyper-saline environment and in the present environment).If you have done any "fitness cost" testing in this area of investigation we would greatly appreciate your to know results so that we know the truth regarding this matter. With Respect, Phil C.bornagain77_{May 28, 2008
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I noticed antibiodic resistance bacteria was another topic being discussed. Evolutionists love to hide the fact that once the bacteria becomes resistant to the antibiodics, it also gets so worn down that the mutation causes them to die when there put with bacteria that havent been exposed. So really the mutation caused them to die.tallmang_{May 27, 2008
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Hello everyone I'm knew on this site and I've gained a strong interest over the last year intelligent design. Just a fact regarding the controversy of this theory that I think is always worth metioning, the verdict of the so called "historical trial" of judge jones was pretty much a direct cut and paste from the ACLU. Yet you have people who call ID corrupt.tallmang_{May 27, 2008
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bornagain77: "I was thinking I could draw up a rough draft and have you check it for errors." That's OK for me.gpuccio_{May 27, 2008
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This following video may help give you a clearer picture of what type of testing I'm looking for in this case: Is antibiotic resistance evidence for Darwinian evolution? http://www.youtube.com/watch?v=rYaU4moNEBU Hope it helps Let me know what you think. I was thinking I could draw up a rough draft and have you check it for errors.bornagain77_{May 27, 2008
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bornagain77: I'll give some thought to that, but I must confess that I have no clear idea of what form such a "fitness test" could practically have (apart form just cultivating the two strains together, which would probably show nothing). I am not a microbiologist, but I think that the concept of fitness is strictly dependent from a specific environment.gpuccio_{May 27, 2008
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gpuccio, All sub-speciation events, that I have seen proof of, occur because of loss of genetic information. While you are correct in bacteria having a tremendous ability to resist change we still find that: We find that 2-9-3 differs from a modern halophile, Salibacillus marismortui, by just 3 unambiguous bp in 16S rDNA, versus the approximately 59 bp that would be expected if these bacteria evolved at the same rate as other bacteria. Thus if just one section of the genome has suffered a 3 bp substitution then I am inclined to think a small but measurable amount of genetic entropy has occured since the parent strain was introduced by God that will show up in a head to head fitness test with all nacent "sub-species". As well, Antibiotic resistant bacteria cannot even compete with the parent strain after only one mutation in head to head fitness tests(compensatory mutations not withstanding). Also, Remember the trench warfare, that was measurable by Behe, that occurred in malaria with just a couple point mutations. Even if fitness is equal in the bacteria I would still like to know the correct answer for the tests. As far as you perhaps helping me; if you know how to properly word the question yourself or if you know someone of Vreeland's stature who could ask him if he has done comparitive fitness tests, I think I would be much more likely to get a responce from him than if I asked in my severely limited language. If I wrote it he would most likely laugh at some stupid wording I accidently used. If you decide to help or to ask someone to help here is his e-mail; Vreeland RH, Rosenzweig WD, Lowenstein T, Satterfield C, Ventosa A. Department of Biology, West Chester University, West Chester, PA 19383, USA. rvreeland@wcupa.edubornagain77_{May 27, 2008
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bornagain77: I don't know... Let me know more in detail what kind of help you need. If I can, I will be happy to help you. You see, the fact is that there seems to be not great genomic difference between the old and the new bacteria. It is not even a speciation. They are the same species, with some differences. My impression is that bacteria and archea of today are probably very similar to those of 4 billion years ago. I understand your point about genetic entropy, but don't you thing that genomes are able to defend, in many ways, their precious information? Maybe they are more efficient than we think in doing that.gpuccio_{May 27, 2008
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gpuccio, I wonder if you think that Vreeland will mind someone writing and asking if he has performed fitness test between ancient and modern bacteria. I wouldn't want too since I will most likely use the wrong wording for molecular-biology, but if you think he will not mind someone asking, Do you think you could help me in getting an answer from him?bornagain77_{May 27, 2008
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Lormy, Many times naturalists will offer “conclusive” proof for evolution by showing bacteria that have become resistant to a certain antibiotics such as penicillin. When penicillin was first discovered, all the gram positive cocci were susceptible to it. Now 40% of the bacteria Strep pneumo are resistant. Yet, the mutation to DNA that makes Strep pneumo resistant to penicillin results in the loss of a protein function for the bacteria (called, in the usual utilitarian manner, penicillin-binding-protein). A mutation occurred in the DNA leading to a bacterial protein that no longer interacts with the antibiotic and the bacteria survive. Although they survive well in this environment, it has come at a cost. The altered protein is less efficient in performing its normal function. In an environment without antibiotics, the non-mutant bacteria survive better because the mutant bacteria cannot compete as well. So as you can see, the bacteria did adapt, but it came at a loss of function in a protein of the bacteria, loss of genetic information in the DNA of the bacteria, and it also lessened the bacteria's overall fitness for survival. Scientifically, it is better to say that the bacteria devolved in accordance with the principle of genetic entropy, instead of evolved against this primary principle of how “poly-constrained information” will act in organisms (Sanford; Genetic Entropy 2005)(Dembski Conservation of Information). As well, all other observed adaptations of bacteria to “new” environments have been proven to be the result of such degrading of preexisting molecular abilities. This following articles have lists of how different bacteria have been degraded in developing resistance for the different antibiotics that have been developed by man: Is Bacterial Resistance to Antibiotics an Appropriate Example of Evolutionary Change? http://www.trueorigin.org/bacteria01.asp http://www.trueorigin.org/camplist.asp excerpt; Table I. Mutation Phenotypes Leading to Resistances of Specific Antibiotics. Antibiotic Phenotype Providing Resistance Actinonin -Loss of enzyme activity Ampicillin -SOS response halting cell division Azithromycin -Loss of a regulatory protein Chloramphenicol -Reduced formation of a porin or a regulatory protein Ciprofloxacin -Loss of a porin or loss of a regulatory protein Erythromycin -Reduced affinity to 23S rRNA or loss of a regulatory protein Fluoroquinolones -Loss of affinity to gyrase Imioenem -Reduced formation of a porin Kanamycin -Reduced formation of a transport protein Nalidixic Acid Loss or inactivation of a regulatory protein Rifampin -Loss of affinity to RNA polymerase Streptomycin -Reduced affinity to 16S rRNA or reduction of transport activity Tetracycline -Reduced formation of a porin or a regulatory protein Zittermicin A -Loss of proton motive force Hope that helps Lormy.bornagain77_{May 27, 2008
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bornagain77 said:
As demonstrated repeatidly with antibiotic resistance this increased fitness to a “hostile” environment always comes at a loss of overall functionality of the bacteria (most times with single point mutations).
What "overall functionality" are you referring to? The primary business of bacteria is sustenance and reproduction, and if antibiotic resistance promotes those (and it undeniably does), what "functionality" suffers?Lormy Kathorpa_{May 27, 2008
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gpuccio, you state: Frankly, I don’t think they have done any fitness test. They probably know well, as do I, that the fitness would be exactly the same. This is where I somewhat disagree with you, for the most likely highly polyconstrained nature of the information in the genome will warrant that a loss of information will accompany the sub-speciation. As demonstrated repeatidly with antibiotic resistance this increased fitness to a "hostile" environment always comes at a loss of overall functionality of the bacteria (most times with single point mutations). Thus I feel strongly that any bacteria that has been degraded through several hostile environments over millions of years will demonstrate a consistent loss of fitness from the parent strain since the genome has been degraded several times over that millions of years by differing environmental factors. The possibility is very real that Genetic Entropy will by demonstrated conclusively even in the sub-species "native' environment because of this factor.bornagain77_{May 27, 2008
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cont. from this study Fatty acid and DNA analyses of Permian bacteria isolated from ancient; The di?erences between 2-9-3 and V. marismortui could certainly be the result of di?erences in gene content, a hypothesis readily testable with modern genomic technology. In fact, based upon the data being obtained during numerous comparisons of the four Permian organisms and V. marismortui sequencing the entire genome of these microbes may be the only way to determine the exact degree of relatedness between these organisms. Another possibility might be that free- living microbes in low nutrient, hypersaline environments may be evolving at rates that are slower than those calculated from other cultures. There is certainly no doubt that bacteria possess the capacity for rapid evolution and di?erentiation (No doubt of rapid evolution?). One need only look to such things as antibiotic resistance (LOL) and biodegradation for con?rmation. However, having the capacity to change rapidly does not necessarily require that one do so. In the months since their initial publication, the data and claims about Permian microbes (Vreeland et al.2000) have been intensely questioned and scrutinized as has been described above. The data presented here show unequivocal di?erences between four Permian strains and microbes isolated from present day environments. In addition, the geological evidence (Vreeland et al.2000; Powers et al.2001; Satter?eld et al.2005) supports the 250-million year age of the salt crystals. The data show that these bacteria are not identical. They are most likely related at the subspecies level. These data do help to rule out questions of contamination by putatively modern strains during the original isolation. It seems Vreeland has really done his science, but I still don't see the fitness test with the suspected sub-species.bornagain77_{May 27, 2008
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bornagain77: Frankly, I don't think they have done any fitness test. They probably know well, as do I, that the fitness would be exactly the same.gpuccio_{May 27, 2008
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Fatty acid and DNA analyses of Permian bacteria isolated from ancient www.wcupa.edu/abi/Extremophiles_Vreeland_et_al.pdf This following study has some hard numbers for what evolution expects for ancient bacteria and what is actually observed for the suspected 250 million year old bacteria. http://www.ncbi.nlm.nih.gov/pubmed/11734907 abstract: Curiously modern DNA for a "250 million-year-old" bacterium. Nickle DC, Learn GH, Rain MW, Mullins JI, Mittler JE. Studies of ancient DNA have attracted considerable attention in scientific journals and the popular press. Several of the more extreme claims for ancient DNA have been questioned on biochemical grounds (i.e., DNA surviving longer than expected) and evolutionary grounds (i.e., nucleotide substitution patterns not matching theoretical expectations for ancient DNA). A recent letter to Nature from Vreeland et al. (2000), however, tops all others with respect to age and condition of the specimen. These researchers extracted and cultured a bacterium from an inclusion body from what they claim is a 250 million-year (Myr)-old salt crystal. If substantiated, this observation could fundamentally alter views about bacterial physiology, ecology and evolution. Here we report on molecular evolutionary analyses of the 16S rDNA from this specimen. We find that 2-9-3 differs from a modern halophile, Salibacillus marismortui, by just 3 unambiguous bp in 16S rDNA, versus the approximately 59 bp that would be expected if these bacteria evolved at the same rate as other bacteria. We show, using a Poisson distribution, that unless it can be shown that S. marismortui evolves 5 to 10 times more slowly than other bacteria for which 16S rDNA substitution rates have been established, Vreeland et al.'s claim would be rejected at the 0.05 level. Also, a molecular clock test and a relative rates test fail to substantiate Vreeland et al.'s claim that strain 2-9-3 is a 250-Myr-old bacterium. The report of Vreeland et al. thus falls into a long series of suspect ancient DNA studies. (the only thing that I think is suspect in the whole thing is the evolutionary theory) The controversy over exact age continued as reported in this site: http://scienceweek.com/2005/sw051118-1.htm But the research group that discovered the (ancient) bacterium has followed up the original report with publications that seek to counter each of these criticisms. In 2002, the group reported their calculation that the degree of genetic damage caused by normal traces of radioactive potassium-40 in the surrounding rock was not great enough to rule out a quarter-billion years of bacterial survival. Yet Vreeland is quite the scientist and conducted this following study to further solidify his claim for 250 million years ago against criticisms of recent deposit of the "ancient bacteria.. New evidence for 250 Ma age of halotolerant bacterium from a Permian Salt Crystal (2005) http://cache.search.yahoo-ht2.akadns.net/search/cache?ei=UTF-8&p=vreeland+New+Evidence+for+250+million-year+age+of+halotolerant+bacterium&y=Search&fr=yfp-t-501&u=cosmology.berkeley.edu/pipermail/duselscience/attachments/20050415/300892fb/CindyGeologypaper-0001.pdf&w=vreeland+new+evidence+250+million+year+age+halotolerant+bacterium&d=FqtqYjWxQij7&icp=1&.intl=us excerpt: CONCLUSIONS We conclude that the halite cement crystals at 564 m in the Salado Formation formed syn- depositionally in shallow subsurface cavities by evaporative concentration of Late Permian seawater. It was in such an environment that the ?uid inclusion and the spore of Virgiba- cillus sp. 2–9-3 were likely trapped in the ha- lite crystal cement. These results con?ne the age of trapping of Virgibacillus sp. 2–9-3, as- suming entrapment in a brine inclusion, to the time of deposition of the Salado salts, 250 Ma. --- I still did not see a fitness test done with its modern decendent. It seems they are more worried whether it is actually 250 million years old than if it will demonstrate a fitness increase. Am I missing something gpuccio? anyone? Surely they would have performed the test for fitness don't you think?bornagain77_{May 27, 2008
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