E. coli and their evolution

_{idnet.com.au
December 5, 2007

Intelligent Design

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Intelligent Design}

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I have been thinking about E. coli and their evolution.

E. coli live in the gut. They are passed environmentally from parents to children.

When humans and baboons had their presumed common ancestor ~ 20 mill years ago, that should be the last time when E. coli in our bowel had a common ancestor with E. coli in the bowel of baboons in the wild.

The following study looked at Baboon and Human E. coli (1985).

“The biotype data indicate that the amount and distribution of genetic variation in the E. coli among free-ranging baboon troops are similar to those in isolates from humans. However, E. coli isolates from baboons are able to utilize a greater variety of sugars as their sole carbon source, possibly because of a greater variety of sugars in the baboon diet.”

If we sequence the E. coli from wild baboons and “wild” humans we should be able to see what evolution can achieve. We already know gene transfer plays a role in gut bacteria.

As an ID supporter I predict that there will be extra genes in baboon E. coli and extra genes in human E. coli but that the origin of these functioning genes will be gene transfer. There should be some random neutral mutations in the other E. coli genes as there have been about 3X10^9 generations of separate development. Of special interest would be the flagellar genes.

What do you think of my predictions? Can ID make predictions? Is ID testable? Will anyone do this experiment?

Comments

Davescot, you need to recognize dog- there could be all kinds of stuff going on in other dimentions that we dont even know about. It is matter that is suspended inspace that makes the whole thing work- I mean look I dont think that this whole universe just went "poof" and unrolled a bunch of super SC- I think it is far more likly that there were processes inside of the universe relative in time and space to one another that interected to form the SC. Im not a big "Poof" its a tiger guy- that is either by DE or ID- i think you probably had matter that was transformed and built via inter-universal injections of information through a different dimention. It was somthing that Michio Kaku one said that brought this idea to my attention- Dembski said in NFL that information can in theory be introduced into matter wihtout adding any energy. Kaku pointed out once in a documentry about UFO's that the shortest path between two points is not a straight line or any string at all but a hole. A worm hole can in effect introduce information into the universe from somewhere else without having to be part of the physical universe- this way information could be downloaded "directly" requiring no wave length. Just an Idea but I like it better than front loaded design becasue this way we can look for more design along the way and the possiblity of an active ID working from time to time in our universe.Frost122585_{December 8, 2007
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Jerry, neo-Darwinism is completely inconsistent with the molecular evidence we now have. Genetic Entropy is completely incompatable with neo-Darwinism. For you to try to make some kind of peace, with the fallacy that blind purposeless processes (neo-Darwinist scenarios) are producing outstanding and stunning complexity on the molecular level, is far beyond me. If anything I will staunchly argue that neo-Darwinism severely pollutes a pure view for what is truly happening on the molecular level, for that is, IN FACT, what neo-Darwinism is actually doing. Shoot Jerry, neo-Darwinism isn't even consistent with the fossil record (that is why punctuated equilibrium was postulated) I ask you, "How in the world is a known fallacy going to help medical research?" The last time I checked lies were a bad thing! I have no problem with natural selection (in fact I suspect an environmental feedback loop to the genome in the natural selection process of favorable adaptations to explain the speed of favorable adaptations), but the fact is that CSI IS in fact being degraded with each and every observed favorable adaptation we are seeing...I repeat and I stress this principle of Genetic Entropy (degradation of the genome) is completely inconsistent with what neo-Darwinism predicts and expects for complexity being generated. In fact in my long response to you, which you claim you read but clearly did not understand, you stated; "My guess is that genetic entropy is entirely consistent with neo Darwinism. I see no reason why it isn’t." This statement of yours is so blatantly wrong I really don't know where to start to try to correct you in this matter. How in the world is a theory that predicts no complexity will ever be generated without intelligence, and that all favorable adaptations to new environments will result in loss of CSI, comparable with a theory that says fantastic complexity can be generated by natural processes with no problem. Shoot man, you even said this: "ID is completely consistent with neo Darwinism as a science." What amazes me is that you actually believe that. Man I can't even write any more you got me so upset.bornagain77_{December 8, 2007
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congregate I was not non-responsive. I clearly stated the distinction between chance and design is made by statistical analysis. That's as much as can be said until an actual case is observed so we have something to analyze. I doubt we will ever make such an observation because I don't think the designer(s) of life are active in the process anymore and the best explanation is that life was front-loaded billions of years ago with all the complexity extant today and all the time since then has been an unfolding of a pre-planned phylogenesis with no subsequent intervention or design input. The case of P.falciparum is important because it is the largest test of evolutionary mechanisms in progress that we have available to study. No other eukaryote anywhere near as well studied as P.falciparum and that has replicated as many times while under observation exists. Even better the organism has been subjected to intense selection pressures by both man-made and natural obstacles to its survival. It is revealing to see which obstacles were overcome, which were not, and exactly how it was able to overcome some of those obstacles.DaveScot_{December 8, 2007
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Any one who criticized what I said about neo Darwinism should learn about neo Darwinism and what I have actually said about it. ID is completely consistent with neo Darwinism as a science. Mutations do happen and are a major concern for modern medicine, natural selection and genetic drift do happen, allele frequencies in population change and medical health is affected by these processes. All are easily demonstrated. All are very relevant for modern medicine. I never said it had much to do with evolutionary biology. I believe people here need to upgrade their reading comprehension skills. Everybody is too quick to criticize as oppose to think. bornagain77 wrote a long comment completely unrelated to anything I said on this thread or have ever said at any time in the past on this blog. I read his comments though apparently doesn't read mine. My guess is that genetic entropy is entirely consistent with neo Darwinism. I see no reason why it isn't. As I continually say, neo Darwinism has a lot relevance for medical science but only explains trivial things in terms of evolutionary biology. This statement is unchallengeable because it fits the evidence closely. But if anyone wishes to respond, read what has actually been said. What is the basis for my statement? Behe's Edge of Evolution for starters. It is an extensive discussion of the relevance of neo Darwinism.jerry_{December 7, 2007
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42 DaveScot- Your response is, well, nonresponsive.
Since we haven’t made the observation you speculate about why don’t we talk about an actual observation.
I was asking about the observation idnet.com.au speculated about. idnet.com.au claimed that evolution of some complexity within three million generations would significantly undercut ID. I don't see how it would do so if ID has the same capabilities as RM+NS, plus more. With regard to the observations you discuss, I don't understand why one set of real world data, the genetic history of one organism over a period of a few score years, is so convincing to you. Why is that? Is there good reason to believe that the current genetic state of P. falciparum and the environment in which that genetic history occurred are so representative of all of the history of life that the results should be taken as conclusively settling the capability of unguided evolution? For that matter, how can any observation provide evidence for the limits of evolution if a designer might have intervened at any point? Perhaps RM + NS was on the verge of making a significant change at some point, but a designer stepped in and redirected the process. If we allow for an omnipotent or "nonmaterial" designer, there can be no conclusive determination of what RM + NS is capable of, can there?congregate_{December 7, 2007
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NDE must be able to perform something impressive in that amount of generations.
Wouldn't we only expect 'NDE' to perform something impressive in that amount of generations if the environment those E. coli find themselves in were to change? You know, things like available sugars would be one such change in the environment, so we'd expect changes in genes that metabolize these sugars. But this expectation is true whether you look at it with ID eyes or with NDE eyes, is it not? Yet, I really don't understand why you would expect changes in flagellar genes (again ID or NDE is irrelevant). Do you think the environment inside a baboon is significantly different from a human such that a different flagellum would be advantageous? Finally, I have to admit that I also do not understand why lateral gene transfer is submitted as an 'ID mechanism' and not part of NDE. Does NDE have some problem with LGT? Has it been shown that a potential designer uses LGT to design? So I really don't understand why you would look at changes inhrun0815_{December 7, 2007
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jdd I am saying nothing of the sort. I am saying much as Prof Behe says, that NDE does not achieve much of substance. The experiment (which I hope might be done) extends the time and opportunities for NDE to produce the goods to 3 billion generations of E. coli. NDE must be able to perform something impressive in that amount of generations.idnet.com.au_{December 7, 2007
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idnet, again I am a little confused. Are you saying that all LGT is the result of ID?? I am not sure how LG is in conflict with NDE. thanks, jjdd_{December 7, 2007
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"NDE is the basis for much of modern medicine and is no threat to ID and evolution. People here should embrace neo Darwinism but separate its value for medicine from evolutionary biology.” What nonsense.pk4_paul_{December 7, 2007
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Jerry "NDE is the basis for much of modern medicine and is no threat to ID and evolution. People here should embrace neo Darwinism but separate its value for medicine from evolutionary biology." I differ with you on the value of NDE to medicine. Antibiotic resistance was attributed to NDE. It kept research at bay for a long time because most resistance is actually due to plasmid gene transfer not NDE. Antibiotic resistance is still the champion of many texts when they look for "evidence" of NDE. To embrace neo Darwinism is a mistake. NDE is a way of explaining what we see in the biosphere. It does not explain the vast majority of what we see. Natural Selection is not in dispute. The power of Natural Selection to create complex specified information is in dispute. Everything non trivial in biology depends on CSI. NDE has no mechanism for generating CSI.idnet.com.au_{December 7, 2007
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Jerry, let's see where the evidence lines up and see if what I assert has any merit. Behe found no evidence of complexity being generated in living organisms by RV/NS in far greater replication/mutation events than have occurred since mammals are supposed to have split from reptiles. As DaveScot pointed out, when this evidence is extrapolated to more complex organisms, we have no reason to believe that random processes are generating complexity for higher life-forms without intelligence. Or as he says: "With this real world data regarding the performance of RM+NS in hand we’re still expected to take it on faith that with orders of magnitude fewer replications RM+NS somehow generated a plethora extremely complex novel proteins and attendant regulatory mechanisms that morphed reptiles into mammals. Non sequitur." As well the fossil record and all other evidence I can find supports the ID implementation at level of parent species with loss of information (Genetic Entropy) being the rule for all successful adaptations/radiations of sub-species. "As Niles Eldredge and Stephen Jay Gould pointed out almost three decades ago, the general pattern for the evolution of diversity (as shown by the fossil record) follows precisely this pattern: a burst of rapid diversity following a major ecological change, and then a gradual decline in diversity over relatively long periods of time." Allen MacNeill PhD (teaches evolution) But, lo and behold, Jerry that pattern fits the front-loaded ID followed by Genetic entropy mo^del to a tee. Allan MacNeill used cichlids to say evolution is currently happening but let's take real a close look at what is happening with cichlids. African cichlid fish: a system in adaptive radiation research http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1635482 of special note: Interestingly, ecological opportunity (the availability of an unoccupied adaptive zone), though explaining rates of diversification in radiating lineages, is alone not sufficient to predict whether a radiation occurs. The available data suggest that the propensity to undergo adaptive radiation in lakes evolved sequentially along one branch in the phylogenetic tree of African cichlids, but is completely absent in other lineages. Instead of attributing the propensity for intralacustrine speciation to morphological or behavioural innovations, it is tempting to speculate that the propensity is explained by genomic properties that reflect a history of repeated episodes of lacustrine radiation: the propensity to radiate was significantly higher in lineages whose precursors emerged from more ancient adaptive radiations than in other lineages. Jerry, all that means that the closer to the parent species that the sub-species is, the better chance it has for a successful radiation into a new ecological niche, Thus conforming to ID/Genetic Entropy as well as having no explanation from the evolutionary theory. (another evolutionary OOPS you could say) This following study shines a very powerful light on what I'm saying about the ID/Genetic Entropy : A Cambrian Peak in Morphological Variation Within Trilobite Species Mark Webster http://www.sciencemag.org/cgi/content/abstract/317/5837/499 http://www.geotimes.org/july07/article.html?id=WebExtra072707.html Jerry in this study Webster studies Trilobites over their 270 million year history in the fossil record! What Did he find? Webster compiled morphological data for nearly 1,000 of the 17,000 different species of trilobites, a class of marine arthropods that died out by 250 million years ago, from 49 previously published sources. By tracking different morphological features — the number of body segments, for example — Webster found that trilobite species exhibited more variation during the Cambrian than in later periods, he reported in Science July 27. "Once you go beyond the Cambrian, the diversity of forms within any one species drops off," he says. That's ID/Genetic Entropy to a tee Jerry. Why did evolution peter out Jerry. 270 million years is a long time for evolution to strut its almighty stuff Jerry! I guess it just got bashful. AGAIN. Tishkoff; Andrew Clark, Penn State; Kenneth Kidd, Yale University; Giovanni Destro-Bisol, University “La Sapienza,” Rome, and Himla Soodyall and Trefor Jenkins, WITS University, South Africa, looked at three locations on DNA samples from 13 to 18 populations in Africa and 30 to 45 populations in the remainder of the world. “We found an enormous amount of diversity within and between the African populations, and we found much less diversity in non-African populations,” Tishkoff told attendees today (Jan. 22) at the annual meeting of the American Association for the Advancement of Science in Anaheim. “Only a small subset of the diversity in Africa is found in Europe and the Middle East, and an even narrower set is found in American Indian. That is Genetic Entropy Jerry. SHHHH, don’t tell that more evolved scientist (Watson) that he actually has less genetic information than Africans! In this following study, for ancient human DNA, we have clear evidence of Genetic Entropy being obeyed!: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=33358 Of special note: Adcock et al. (7) clearly demonstrate the actual extinction of an ancient mtDNA lineage belonging to an anatomically modern human, because this lineage is not found in living Australians. Although the fossil evidence provides evidence of the continuity of modern humans over the past 60,000 years, the ancient mtDNA clearly does not, providing an excellent example of why the history of any particular locus or DNA sequence does not necessarily represent the history of a population. Adcock et al.’s They could not believe the loss of information happened thus they said the "continuous" fossil record was wrong. OOPS on evolution again. That's ID/Genetic Entropy to a tee Jerry. As well fossilized plants follow the pattern for ID?Genetic Entropy: At one of the few petrified forests that sports ginkgo wood, I was told by the naturalist that ginkgos are old in the fossil record—they date from the Permian back when trees were first “invented”. She said that there are a number of species of fossilized Ginkgoaceae, with Ginkgo biloba, the only living (surviving) species, being one of them. That is Genetic Entropy to a tee Jerry. Here is a Paper that has confirmation of dogs and grey wolves staying within principle of Genetic Entropy. http://jhered.oxfordjournals.org/cgi/reprint/90/1/71.pdf of special note: Some sequences found in dogs were identical to those in wolves… The sequence divergence within dogs was surprisingly large: the mean sequence divergence in dogs 2.06 + or - 0.07% was almost identical to the 2.10 + or - 0.04% (sequence divergence) found within wolves. (notice that sequence divergence is slightly smaller for the population of dogs than for the population of wolves) Coupled with the diverse morphology of domesticated dogs and known hazards of dog breeding, this evidence strongly indicates “front loaded adaptations” at a loss of information from parent species. Thus, this is genetic confirmation of the principle of Genetic Entropy for dogs from wolves! Of special note for the Mexican hairless dog (chihuahas); many founder halotypes were likely lost because of "genetic drift" The gene that determines hairlessness is nt but let^hal when homozygous. Thus clearly the "mutation" that causes hairlessness is not a gain in information. This following paper is more recent and more concrete in establishing the principle of Genetic Entropy for dogs/wolves: Origin of dogs traced http://news.bbc.co.uk/2/hi/science/nature/2498669.stm of special note: Their findings, reported in the journal Science, point to the existence of probably three founding females - the so-called "Eves" of the dog world. They conclude that intensive breeding by humans over the last 500 years - not different genetic origins - is responsible for the dramatic differences in appearance among modern dogs. and the paper itself: http://www.sciencemag.org/cgi/content/abstract/298/5598/1610?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=%28Peter+AND+Savolainen+AND+science+AND+old+AND+world+AND+dogs%29&searchid=1&FIRSTINDEX=0&resourcetype=HWCIT Genetic Evidence for an East Asian Origin of Domestic Dogs Peter Savolainen,1* Ya-ping Zhang,2 Jing Luo,2dagger Joakim Lundeberg,1 Thomas Leitner3 The origin of the domestic dog from wolves has been established, but the number of founding events, as well as where and when these occurred, is not known. To address these questions, we examined the mitochondrial DNA (mtDNA) sequence variation among 654 domestic dogs representing all major dog populations worldwide. Although our data indicate several maternal origins from wolf, >95% of all sequences belonged to three phylogenetic groups universally represented at similar frequencies, suggesting a common origin from a single gene pool for all dog populations. A larger genetic variation in East Asia than in other regions and the pattern of phylogeographic variation suggest an East Asian origin for the domestic dog, ~15,000 years ago. How did they trace the lineages? They traced it by the loss of genetic variation (the loss of "front-loaded" information from original parent species) Jerry. That is ID/Gentic Entropy to a tee Jerry. So you can call me uninformed and contentious and say that I'm running a fools errand, but I will stay true to evidence no matter what you think about me, because if you want to believe a lie that is your, God given, American right, just don't drag me along and tell me I have to believe in the fairy tales as you do.bornagain77_{December 7, 2007
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lars: I agree with you that, in principle, an ongoing intervention of the designer is a real possibility, and that could include anything whicho happens both in the lab and in the wild. Obviously, the modalities of the implementation of design are fundamental here, and that's exactly what we don't know, and scientific research could help understand, once the design assumption is more widely accepted. It seems evident that some modalities of design implementation (accasional and sudden, or frontloaded) are less likely to be detected in historical time, while a low-level continuous implementation could be detected more easily. What we certainly know, and I think that is what Behe comments about, is that usually we "don't" detect design implementation in what we observe, both in the lab and in the wild. We just observe random variation in the limits of what can be expected from a random phenomenon, and occasional natural selection of such a trivial variation. That's what Behe's book is about, and that's perfectly consistent with Dembski's theoretical assumptions. Obviously, if we were to witness a clear design implementation, that would be a very good observation to understand how design is introduced in reality. But, if the design implementation happens continuosly, it could be a very low-level phenomenon, and probably we will have to improve greatly our understanding of physical laws before we can really detect it. Anyway, I stay convinced that the problem of design implementation in biological beings is very similar to the problem of the interacion between our consciousness and our body: both are examples of mental properties beong superimposed to matter by conscious beings. Perhaps it's not by chance that Denyse keeps two parallel blogs on those two subjects...gpuccio_{December 7, 2007
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bornagain77, Your are certainly entitled to your beliefs but I believe that neo Darwinism explains a lot of things and I also believe trying to dispute it makes one look uninformed and contentious. Instead point out its limitations but I believe trying to debunk it entirely is a fools errand and very counter productive. Dembski has no problem wtih neo Darwinism, just the Blind Watchmaker Thesis.jerry_{December 7, 2007
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Don't get me wrong -- I'm not saying (#48) that the proposed research is not useful for refuting NDE and advancing ID. As I write and think about it, I'm coming around to the idea that this assumption (that no designer ever, or hardly ever, intervenes in producing new biological systems in recorded history) is necessary for making predictions, even though it doesn't seem to be really a claim of ID. Good to make it explicit though, so that we don't unwittingly promote deism.lars_{December 7, 2007
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BA77 @46, I'm confused by the phrase "ID was implemented", but I think you're telling me this: yes, ID assumes that any that occur in the lab are due to undirected natural causes. (Am I understanding you right?) If so, why should that assumption be made? It doesn't seem to be implied by the premise that design is detectable. Is it just a pragmatic assumption that's deemed necessary for conducting research? Then, where does "the lab" end? Is our recorded medical history of HIV and the malaria parasite in "the lab", even though it occurred out in the real world? Behe apparently considers it so. What about the "3X10^9 generations of separate development" of E. coli over 20-25 million years, that idnet is talking about? He seems to be making the same assumption (I think). And if these are in "the lab", what does the lab not include? Finally, if there is a designer and he decides to introduce some new systems in the middle of your lab experiment, should ID be falsified by that event? Such a falsification condition doesn't seem to me to fit the point of ID very well. This point may seem unimportant to the disagreement between ID and NDE, but I think we should be careful what is predicted in the name of ID, lest ID fail due to excessive modesty! If we really want to follow the evidence wherever it leads, on what basis can we exclude ongoing Designer intervention? Please correct me if I'm misunderstanding the (proposed) direction of ID research.lars_{December 7, 2007
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idnet, 35:
“The sheer magnitude of the differences was totally shocking to us,” says Perna. Though the 0157 strain was recognized only in the last 20 years, it is thought to have diverged from the harmless version some 4.5 million years ago.
Sounds like the 4.5mya was estimated prior to this study, not as a result of finding the 'magnitude of the differences'. So what is the impact of this discovery - that the amount of change was (as they seem to imply) much greater than predicted by the standard evolutionary model? To push back the divergence estimate? To attribute the change to other mechanisms than RM+NS, like gene transfer?
Many of the genes in the 0157-specific islands are thought to have arisen through cross-species transfer from other bacteria.
I wonder if that's an inference from the new data ("RM+NS couldn't have done it so it must have been LGT"), or an independently supported result?lars_{December 7, 2007
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lars, Intelligent Design (CSI) was implemented at the level of parent species with loss of information from parent species upon all favorable sub-speciation events to different environments i.e. You don't have to worry about some unknown complexity being generated in the lab. Adaptations will always conform to Genetic Entropy.bornagain77_{December 7, 2007
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Jerry, I find your comment interesting in that Dr. Behe sought to clarify what evolution could and could not do and was slandered for sticking true to empirical science. No Sir Neo-Darwinism doesn't lead to better practice of modern medicine for it must continually battle what is becoming increasingly obvious to ID proponents. In fact a neo-Darwinists is more likely to investigate bogus areas of research as far as medicine is concerned for his foundational belief, in large scale complexity being generated naturally, is bogus to begin with.bornagain77_{December 7, 2007
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congregate:
But after the research is done, we still won’t know. If new systems arise, how do we distinguish between those that arose through RM and NS and those that arose through an intervening designer?
Yeah, that's bugged me too. It seems like an underlying assumption in Behe's research, and this proposal too, is that whatever we see happening in known history (as opposed to prehistory) can safely be attributed to natural causes, not a designer. But if we accept a designer that worked in prehistory, why should we assume that he/it must have stopped working in observable history? There's no reason to. However, if you look at it conversely, I think the research makes more sense: if undirected causes (RM+NS) are responsible for producing complex new systems, then they should continue to produce new functions the same way in observable history as they supposedly did in producing all these amazing systems. If new function does not arise in the time NDE predicts it should, or if such new function arises solely due to other causes (like lateral gene transfer), then that disconfirms the ability of RM+NS to produce new function as laid out by NDE. The latter effect then supports ID as the only viable alternative, whether in history or prehistory or both.lars_{December 7, 2007
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Seekandfind, You said "That’s the popular perception about ID from the elite. There really is a need to overcome this hurdle." and also "2) Understanding Darwinian evolution CAN help us find the cause and possible cure for the spread of diseases like avian flu." The problem would disappear if people stopped harping here on how neo Darwinism has been falsified or is bogus. It gives the impression that it has no value but in reality it is the basis for much of modern medicine and is no threat to ID and evolution. People here should embrace neo Darwinism but separate its value for medicine from evolutionary biology.jerry_{December 7, 2007
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congregate If new systems arise, how do we distinguish between those that arose through RM and NS and those that arose through an intervening designer? To me this is equivalent to asking "if a pink elephant with wings were observed how could we distinguish between chance and design?". Since I never expect to see such a thing it seems like nothing more than wool gathering to discuss it. However, the short answer is we would make the distinction the same way we do for any other case where design is suspected (murder, arson, sabotage, archeological finds, etcetera) - through statistical analysis. Since we haven't made the observation you speculate about why don't we talk about an actual observation. In billions of trillions of replications of P.falciparum where each replication gave RM+NS a chance to make a heritable genetic change we observed exactly what statistical analysis predicted given the number of replications and a background mutation rate of one nucleotide change per billion nucleotides copied - no phenotype change resulted that wasn't limited to at most a few chained interdependent nucleoties. With this real world data regarding the performance of RM+NS in hand we're still expected to take it on faith that with orders of magnitude fewer replications RM+NS somehow generated a plethora extremely complex novel proteins and attendant regulatory mechanisms that morphed reptiles into mammals. Non sequitur.DaveScot_{December 7, 2007
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idnet.com.au at 31:
If E Coli over 3 billion generations can engineer new systems from RM and NS then ID is unlikely to stand. Until we do the research, how will we know?
But after the research is done, we still won't know. If new systems arise, how do we distinguish between those that arose through RM and NS and those that arose through an intervening designer?congregate_{December 7, 2007
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RE: ------------------------------ What do you think of my predictions? Can ID make predictions? Is ID testable? Will anyone do this experiment? ---------------------------- In respect to the E-coli, I think your proposal needs to be taken seriously. One of the biggest hurdles ID faces is the perception that it isn't falsifiable. By extension to that, the other hurdle is this -- because it isn't falsifiable and testable, ID believers teach us nothing about the causes and cure for contagious diseases. Take this editorial from the Wall Street Journal for instance ( written yesterday by Lawrence Krauss, Professor of physics and astronomy at Case Western Reserve University )... First, he decries the fact that on average, our students are being beaten by kids from Asia and other countries in standardized science tests. Then his entire piece is essentially to present the case that we need to encourage our young ones to master the tools that lead to expertise in science. Fair enough. But here's the key sentence that shows his anti-ID bias ( the Wall Street Journal requires registration so I'll have to type the sentence for you ) : "... science and technology will be essential to meet the challenges to face as a society. When reports began to surface warning that the avian flu might become a threat to humans, for example, everyone from the president down called for studies to determine how quickly the virus would mutate from birds to human beings. No one suggested that 'intelligent design' for example, could provide the answer." The unstated assumptions in the above small paragraph are : 1) Belief in ID does nothing to help us find the cause and possible cure for the spread of diseases like avian flu. 2) Understanding Darwinian evolution CAN help us find the cause and possible cure for the spread of diseases like avian flu. 3) Those who believe in ID are backward and a hindrance to scientific progress. That's the popular perception about ID from the elite. There really is a need to overcome this hurdle.SeekAndFind_{December 7, 2007
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It's not totally clear to me that if your prediction were fulfilled, it would unqualifiedly support ID; rather, it would seem to disconfirm NDE. Which is fine, and useful, but I think the distinction should be made explicit, so that Darwinists don't have a basis for saying you're making false claims of testing ID. Basically it would be one more data point along the lines of Behe's research in EoE, showing the poverty of what RM+NS is able to achieve in X number of generations, right? And he already has some data about E. coli, so this would be a nice complement to it. I would like to hear a Darwinist comment on this research proposal: if your prediction were shown correct, would that confirm ID and disconfirm NDE? if your prediction were shown incorrect, would it falsify ID and verify NDE? It would be great to have these reactions in advance, so that we don't have to solicit them in a context of "My prediction was right, so now will you convert to ID?" :-) And as you note, it would also advance the discussion of whether ID, and NDE, are falsifiable or verifiable.lars_{December 7, 2007
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idnet.com.au, I'm still trying to figure out how this prediction fits into the current ID/Genetic Entropy Mo^del: "I predict that there will be extra genes in baboon E. coli and extra genes in human E. coli but that the origin of these functioning genes will be gene transfer." Which particular gene transfer study are you basing this prediction on? Is not this a sub-section of the symbiotic evolution that Dr. Lynn Margulis was trying to popularize in her book "Acquiring Genomes": A Theory of the Origins of Species, I went to the study you cited and found this: "Comparison of O157's sequence with that of its harmless E. coli cousin revealed 1,387 new genes in the virulent version. There are 'DNA islands' of sequences unique to 0157 scattered throughout the genome. Conversely, there are islands in the laboratory E-coli strain containing 530 genes that are not found in 0157." Then I found the total number of genes for E-coli: E. coli 4,639,221 base pairs: 4,377 genes: 4,290 of these genes encode proteins; the rest RNAs. 530+1387= 1917 gene difference of 44.6% between the two different E-coli's That's quite a lot of difference to attribute to solely to "gene transfer". As well, In the ENCODE studies we are finding that a large portion of genomes (at least for higher life forms) appear to be poly-functional thus poly-constrained to this type of radical change you seem to be stipulating for E-coli (Sanford Genetic Entropy pg. 141). I believe that much of the E-coli genome will be also found to be similarly poly-functional and thus poly-constrained to this type of radical change you seem to be predicting for ID. These following articles will give you an indication where I am having problems with your gene transference prediction for ID. http://www.genome.gov/25521554 BETHESDA, Md., Wed., June 13, 2007 - An international research consortium today published a set of papers that promise to reshape our understanding of how the human genome functions. The findings challenge the traditional view of our genetic blueprint as a tidy collection of independent genes, pointing instead to a complex network in which genes, along with regulatory elements and other types of DNA sequences that do not code for proteins, interact in overlapping ways not yet fully understood. http://www.boston.com/news/globe/health_science/articles/2007/09/24/dna_unraveled/?page=1 "The science of life is undergoing changes so jolting that even its top researchers are feeling something akin to shell-shock. Just four years after scientists finished mapping the human genome - the full sequence of 3 billion DNA "letters" folded within every cell - they find themselves confronted by a biological jungle deeper, denser, and more difficult to penetrate than anyone imagined. "Science is just starting to probe the wilderness between genes," said John M. Greally, molecular biologist at New York's Albert Einstein School of Medicine. "Already we're surprised and confounded by a lot of what we're seeing." A slew of recent but unrelated studies of everything from human disease to the workings of yeast suggest that mysterious swaths of molecules - long dismissed as "junk DNA" - may be more important to health and evolution than genes themselves." Thus, as you can see idnet.com.au, gene transference, on such a large scale as you seem to be indicating, is severely problematic with the current state of what is known.bornagain77_{December 7, 2007
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ellazimm, The principle of Genetic Entropy remains intact and robust, even for HIV's trivial gain in complexity. This is because HIV is a non-living "hijacker" into each and every person it infects. HIV trivial gain in complexity destroys far more tremendous complexity each and every time it infects a person. Is complexity in the whole human race lost to HIV's trivial gain in complexity? NO, for HIV has not infected the entire population of humans. Yet Genetic Entropy still remains intact because each and every human being, the HIV interacts with and infects with its new trivial gain in complexity, suffers a severe loss in the integrated complexity necessary for life. I stress that this tremendous complexity is clearly lost, and Genetic Entropy is clearly payed for in infected Humans EACH and EVERY time HIV interacts with a specific infected human. As well, I don't see how HIV is demonstratively any closer to the very tremendous and very specific complexity, that is absolutely necessary to be accomplished, to actually become "alive" and self-sustaining. Unless you can prove how a "passive" ring structure will lead to the very specific complexity necessary for life, I think HIV's perceived violation of Genetic Entropy will be falsified on this front as well. Thus the seeming violation of "Genetic Entropy" in HIV is, when viewed soberly, clearly payed for by the tremendous complexity that is lost in each and every individual infected, each and every time infection occurs.bornagain77_{December 7, 2007
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Slightly Off Topic: I thought this was interesting: New Stem Cell Technique Effects Cure http://www.philly.com/philly/wires/ap/features/science/20071206_ap_newstemcelltechniqueeffectscure.html Scientists have the first evidence that those "reprogrammed stem cells" that made headlines last month really have the potential to treat disease: They used skin from the tails of sick mice to cure the rodents of sickle cell anemia. ...The study, published in the journal Science, doesn't bring this potential therapy closer to people just yet. Big hurdles remain, including a risk of cancer from the reprogramming method. ....The researchers converted those skin cells into iPS (Induced Pluripotent stem) cells by infecting them with viruses engineered to change the skin cell's gene activity so they would resemble embryonic cells. Using DNA splicing techniques in those cells, the researchers then snipped out the small mutated stretches of DNA that cause sickle cell anemia and filled those gaps with bits of DNA bearing the proper genetic code. Next the researchers treated the corrected iPS cells with another kind of virus - this time one "designed" to induce genetic change the cells to mature into bone marrow cells. Finally,, each mouse was given an infusion with the corrected marrow cells created from its own skin cells. Those cells set up permanent residence in the animals bones and began producing blood cells - the major function of marrow cells - and releasing them by the millions into the animals circulatory system. But now the blood cells being produced were free of the sickle cell mutation.bornagain77_{December 7, 2007
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"Comparison of E. coli O157's sequence, the pathogenic bacteria that often infects ground beef, with that of its harmless E. coli cousin revealed 1,387 new genes in the virulent version. There are 'DNA islands' of sequences unique to 0157 scattered throughout the genome. Conversely, there are islands in the laboratory E-coli strain containing 530 genes that are not found in 0157. Many of the genes in the 0157-specific islands are thought to have arisen through cross-species transfer from other bacteria. "The sheer magnitude of the differences was totally shocking to us,'' says Perna. Though the 0157 strain was recognized only in the last 20 years, it is thought to have diverged from the harmless version some 4.5 million years ago. GENOMICS: E-coli Sequence Holds Surprises; Applied Genetics News, Feb, 2001 http://findarticles.com/p/articles/mi_m0DED/is_7_21/ai_70907653idnet.com.au_{December 7, 2007
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"The cost of CGS resequencing services from Nimblegen Systems is currently $7500 per clone for E. coli." Sounds cheap to me.idnet.com.au_{December 7, 2007
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Russ, HIV demonstrated a trivial gain in complexity, but destroyed more complexity from its host life form (us) than it gained. as put by Dr. Behe: Second, the viroporin (of HIV) is not some new molecular machine. There is no evidence that it exerts its effect in, say, an ATP- or energy-dependent manner. Rather, similar to other viroporins, the protein simply forms a passive leaky pore or weak channel. (4,5) This situation is probably best viewed as a foreign protein degrading the integrity of a membrane, rather than performing some positive function. Thus, Since the non-living HIV destroyed more complexity than it gained, The HIV stayed within, what is termed "the principle of Genetic Entropy". As well all other mutations, to living organisms, that are claimed to be beneficial, always "break" something or turn something off (see post 22) to get their so called beneficial adaptation. Thus in truth "Genetic Entropy" is the foundational rule of biology for all advantageous adaptations. That is to say all advantageous adaptations of a sub-species from a parent species to new environment will be found to come at a cost of information from the parent species.bornagain77_{December 6, 2007
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