E. coli and their evolution

_{Mark

December 5, 2007

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

jerry: Here's what Provine (2001) says about the concept of "gene pool": The notion of "gene pools" now strikes me as one of the most artificial concepts of population genetics. What exists in the "gene pool" is vague, but perhaps most often either "genes" or "alleles." Other candidates for the gene pool are chromosomes, gametes, and whole organisms. Neither genes nor alleles float free, but are on chromosomes, and do not cleave every generation. Talking about the cohesion, coadaptation, and homeostasis of the gene pool means attribution of aesthetically desirable characteristics to a non-existing entity. In small populations, invocation of the gene pool as the biological source of the random sampling for genetic drift leads to serious problems. You write: "If neo Darwinism is thought of in this way, without any philosophical baggage about grandiose changes in the genome, it is true and makes a good addition to the ID paradigm." First, I'm not denying the very real molecular effects we see happen in bacterial populations. It is real. Rather, I object to it being called "natural selection" for two reasons: (1) NS is an "effect"; not a "cause" (Provine's exact point) (2) there is no "selection" taking place. In the case of artificial selection, humans, causative beings, are both cause and select outcomes for future breeding; and , so, the term "artificial selection" makes perfect sense. What if instead of calling the process whereby bacteria develop antibacterial resistance "natural selection", we simply term it a "process of adaptation"? Doesn't this truly describe what we see happen? In terms of ID, I simply see---as you propose---this "process of adaptation" as part of the Designer's original design. When it comes to "adaptation" to a particular environment, Mendelian genetics makes sense. It provides for various combinations of factors to interplay with one another in such a way as to allow an appropriate phenotype to emerge, dependent upon the particular environment presently encountered. So, of course, we would see Mendelian genetics at work. Now this may be great for 'eye color'; but what about the 'eye' itself? Would you want it to be subject a whole host of possible combinations, or would you want it to always be expressed? If it is to be always expressed, then what is the need for "alleles"? Provine talks about the "one-locus, two-allele models" this way: The persistence of the one-locus, two-allele models raises a fascinating historical issue. Why have the earliest models of the theoretical population genetics managed to survive almost unscathed into modern textbooks on evolution and genetics? Surely the misleading limitations of these models are understood by evolutionists and geneticists. Do teachers think the students must first learn what they did as students, and later correct these beliefs? I find that most evolutionists and geneticists still adhere to belief in rampant random genetic drift in small populations, which matches their firm belief that natural selection is a mechanism that creates adaptations. In 1970 I could see the origins of theoretical population genetics as being an unalloyed good for evolutionary biology, and thus obviously a great subject for an historian. Now I see these same theoretical models of the early 1930's, still widely used today, as an impediment to understanding evolutionary biology, and their amazing persistence in textbooks and classrooms as a great topic for other historians. The "one-locus, two allele" model was developed in the early part of the 20th century, fifty years before the discovery of DNA. Knowing what we do about genetics, think through this problem: I have thalassemia. I got it from my mother. I have one wrong amino acid in my hemoglobin chain. The protein is defective. Some nucleotide along the string of nucleotides that code for the hemoglobin protein has an error. Here are some questions: (1) the DNA I have comes half from my dad and half from my mom. Since my dad's hemoglobin is natural, that means, assuming my mom and dad's DNA lined up correctly, that the nucleotide from my dad's side of hemoglobin is different from my mom's side of the DNA. So, how did they match up? (2)Was some "correction mechanism" involved? If so, why didn't it correct my mom's DNA instead of my dad's? (3)If my dad's side of the DNA was corrected to match my mom's, then where is the second allele for thalassemia? Is it the complementary side of the hemoglobin string of nucleotides? Or is it at some entirely different portion of the genome? (4)If it is the complementary side, and if my dad's side is being corrected to match my mom's side, then why am I alive, since that would make me "homzygous" for thalassemia---which is lethal in the homozygous form after age 3-4? I think this is why Provine says: "Using these [one-locus, two-allele] models to understand random drift, selection, fitness surfaces, and gene pools is an invitation to misunderstandings. I view these simple models as impediments to understanding evolution in either natural or domestic populations." Let's remember that Mendelian genetics are 150 years old. We need to completely re-think genetics. That's what evo-devo proposes; but, of course, they assume too much pre-existing information to be right on the merits. I think the answer will come from viewing the genome as a complicated software program that has enormous regulating loops. "Junk-DNA" is proving to be the province of these regulatory elements---you know, that 97% of the genome that is "non-coding" (for proteins, but does code for small, interfering RNA's, the secret to the cell's regulatory mechanisms).PaV_{December 11, 2007
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id.net, Thanks for using the "not a specified argument" argument.Frost122585_{December 11, 2007
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PaV, Maybe this should be the subject of another thread some time in the near future. I bet that Provine and MacNeill don't disavow natural selection as uniformly as you say they do. We can certainly ask Allen MacNeill who when he was last here talked extensively about different forms of natural selection. The problem with natural selection is not that it cannot do anything, it does, but that it rarely if ever presented with anything of consequence on which to operate. That I think MacNeill will agree. If a population that had considerable variation in it migrated from the forrest and plains to the dessert, we would probably see a new variant that adapted to the dessert. But it is likely that this species over time would have less variation than the original population. The only way to replenish the gene pool would be by gene flow with mating outside its population. In other words natural selection tends to narrow the gene pool of a population but in the process create species that can adopt to a new environment such as isolated islands. Occasionally a mutation comes along that helps, such a color change of fur, but rarely if never is there any major functional change that arises. In addition to this genetic drift will also reduce the gene pool so both processes narrow the variation in a population. If neo Darwinism is thought of in this way, without any philosophical baggage about grandiose changes in the genome, it is true and makes a good addition to the ID paradigm. And an ID research paradigm will argue that such process are what to be expected by evolution. And such claims of new speciation in such things as cichlids are really just neo Darwinism acting to reduce variation and not increasing it. But this reduced variation results in a species that is better adapted to its environment. But in the long run is the road to extinction because if the environment ever changes it will not be able to handle it.jerry_{December 11, 2007
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Bad at 83 revisited Neo-Darwinian Evolution predicts that RM and NS will achieve major feats. Making a claim that ID theory is wrong or insufficient is not making a positive prediction for Neo-Darwinian Evolution. The core problem with NDE is that it has the potential to explain anything at all. You cannot escape this problem simply by making a bunch of random predictions and then declaring yourself proven correct if some of them happen to come true. The predictions have to flow from some specific and limited range of explanation that your theory supplies. It’s only if NDE theorists are willing to careful specify the proposed mechanisms and their parameters and limitations that we could pick out its actions. But instead, we are left with a cause that can do literally anything in any way at all. Except that we’ve watched new metabolic pathways created by Intelligent Designers in the lab, and especially in bacteria: and so commonly observed that it’s not even of particular note anymore. There IS a sort of evidence however, that would make it extremely obvious that a NDE was involved: if whole functional systems arose in one species without any method of transmission via contact with plasmids or LGT from other species. Claiming and showing are not the same things.idnet.com.au_{December 11, 2007
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"The core problem with ID is that it has the potential to explain anything at all." This is the pan calling the kettle black. Let's remember that ID predicted that "junk-DNA" would turn out not to be junk. The neo-Darwinist scenario was that all this non-coding DNA was just left-over stuff. Neo-Darwinism gets this prediction wrong, and, it's as if nothing at all has happened. We hear a collective, "Oh well...." Sorry. That won't work.PaV_{December 9, 2007
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William Provine believed that natural selection was the null hypothesis for all evolutionary change in the 60's. In 2001, he believed that natural selection did absolutely nothing. There's been a lot of science done since the 60's. It changed Provine's mind---an emminent population geneticist; why shouldn't it change ours? Or, at least allow us to suspend judgment on what we are spoon-fed by the neo-Darwinists? I'm perfectly comfortable with Darwinism (macroevolution)---if it is proved to be correct science. I'm perfectly comfortable with neo-Darwinism (microevolution)---if it holds up as correct science. I just personally happen to believe that there are a lot of surprises ahead, and that with these surprises, natural selection will seen, in the end, to "do nothing", just as Provine now asserts. In the meantime, I'm not ready to concede much.PaV_{December 9, 2007
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It’s only if ID theorists are willing to careful specify a sort of designer and its parameters and limitations that we could pick out its actions.
The beauty of a design inference is that it can be had without knowing anything about the designer(s). Obviously the parameters and limitations are the physical laws that govern our universe. See also: Intelligent Design: The Design HypothesisJoseph_{December 9, 2007
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StephenB, I believe we are all God's children made in his image. To me metaphysical materialism is pap for the uninformed which is what I consider atheists. Atheism is intellectual bankruptcy and the mark of one who is lazy or dishonest. However, for the most part I stick to science on this blog because discussing philosophy and religion gets in the way of what has to be accomplished.jerry_{December 9, 2007
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Jerry: What is your philosophical position seperate from science? Do you accept metphysical materialsm/naturalism or some form of it.StephenB_{December 9, 2007
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Yes. ID predicts that RM and NS will achieve only very minor feats.
Making a claim that some other theory is wrong or insufficient is not making a positive prediction for your theory. The core problem with ID is that it has the potential to explain anything at all. You cannot escape this problem simply by making a bunch of random predictions and then declaring yourself proven correct if some of them happen to come true. The predictions have to flow from some specific and limited range of explanation that your theory supplies. It's only if ID theorists are willing to careful specify a sort of designer and its parameters and limitations that we could pick out its actions. But instead, we are left with a cause that can do literally anything in any way at all.
This may enable processing a substrate with a slightly different side chain at most. ID theory suggests that totally new metabolic pathways and molecular machines do not arise by RM and NS.
Except that we've watched new metabolic pathways evolve in the lab, and especially in bacteria: and so commonly observed that it's not even of particular note anymore. It's also worth noting that known instances of Lateral Gene Transfer, since the mechanisms are almost always related to virii or error, works as just a different source of mutation. There IS a sort of lateral gene transfer however, that would make it extremely obvious that a designer was involved: if whole functional systems were transferred from one species to another completely different species in another taxa without any method of transmission via contact (the most common, and the only one reliably used by evolution being through ancestry). Human geneticists can already do this even with our primitive techniques. And yet this sort of thing is stunningly absent from nature, as are most of the ways in which the design of an intelligent designer could be made extremely conspicuous.
magnan: Secondly, Behe in TEOE shows how E. coli, HIV and Plasmodium Falciparum in recent historical time failed to create significant new complex innovative structures and mechanisms despite astronomical numbers of replications.
Claiming and showing are not the same things. Behe's book is a lot less convincing than actual people who study these virii and bacteria, and say that Behe is, in fact, wrong about this.Bad_{December 9, 2007
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77 Telic-meme (#77), thanks for an interesting link. This does seem to be a research study proposal with certain very limited ID implications. It definitely is looking to find a form of Endogenous Adaptive Mutagenesis (EAM) in microorganisms. Hypothesis 1 if confirmed would show that the bacteria can increase the frequency of certain types of mutation in response to stressors. A research paper that offers some evidence for this along with important applications to antibioic research was posted on another thread. This is Cirz RT, Chin JK, Andes DR, de Crécy-Lagard V, Craig WA, et al. (2005) Inhibition of Mutation and Combating the Evolution of Antibiotic Resistance. PLoS Biology 3(6): e176 doi:10.1371/journal.pbio.0030176. Hypotheses 2 and 3 if confirmed would show some sort of epigenetic control mechanism in the bacteria that "directs" certain types and locations of mutation in response to certain stressors, based on the "need" of the microorganism to change particular expressed proteins. It isn't clear to me how confirmation of Hypothesis 3 would advance ID theory, however. Being a mechanism, however complex, it couldn't act as a teleological intelligent agent in originating IC biological structures. One of the core arguments of ID is that the IC and CSI of life inherently demand such an influence. Secondly, Behe in TEOE shows how E. coli, HIV and Plasmodium Falciparum in recent historical time failed to create significant new complex innovative structures and mechanisms despite astronomical numbers of replications. Behe points out that this shows an inherent limit to the power of undirected Darwinist mechanisms. If the bacteria have EAM mechanisms such as suggested in the research proposal, then they must have been operating during the long term studies cited by Behe. The very limited results would seem to show the very limited power of whatever EAM mechanisms exist in creating innovation.magnan_{December 9, 2007
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PaV, What do you mean by "Should we be going back to the 1960’s?"jerry_{December 9, 2007
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[Don't know what happened. I hit something and the above just posted. Here's the quote] 1. Natural selection was the primary mechanism at every level of the evolutionary process. For any change in an adaptation or gene frequencies, natural selection was the null hypothesis." Then, in 2001: "As John Endler has argued eloquently in Natural Selection in the Wild (1986), natural selection is not a mechanism. Natural selection does not act on anything, nor does it select (for, or against), force, maximize, create, modify, shape, operate, drive, favor, maintain, push, or adjust. Natural selection does nothing. Natural selection as a natural force belongs in the insubstantial category already populated by the Becker/Sthal phlogiston (Endler 1986) or Newton's 'ether'. . . . Having natural selection select is nifty because it excuses the necessity of talking about the actual cuasation of natural selection. . . . . . . . The chances are small that a particular DNA sequence in mammals is 'adapted through natural selection'. The chances are great that the evolution of selectively neutral factors produced the sequence. Thus at the DNA level, explaining any random sequence invokes selectively neutral or nearly neutral factors as the null hypothesis, an amazing turnabout since the late 1960's. I now argue that each level (phenotypic, protein, and DNA sequence) marches to different drummers." Should we be going back to the 1960's?PaV_{December 9, 2007
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I'm gone for the rest of the day, but let me just add the following: 1.) Neo-Darwinism=RM+NS 2.) Are mutations random? Well, yes and no. Do they happen in a random fashion? Yes. Are they completely random? No. Why do I say that? Because we now know that bacteria under stress "increase" their mutation rate, and the increase rate occurs in specific areas of the genome. Well, how does that happen? I suspect that bacteria simply shuts down the normal error-correction-mechanism for these specific areas of their genome. If, indeed, this is the mechanism, would it be correct to call this overall process 'random'? I don't think so. 3.) Here's what Willian B. Provine writes in the "Afterword" of the re-issue of his "The Origins of Theoretical Population Genetics." (jerry: neo-Darwinism=population genetics + inordinate extrapolation): "MY VIEWS IN 1959-70 1.PaV_{December 9, 2007
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I personally believe that ID should embrace neo Darwinism for two very important reasons 1. It describes a process that produces a lot of change in living organisms and these changes have highly significant effects on life's progress. Consequently, it is foolish to rail against it. 2. I believe it is part of the design of life and as such is totally in sync with ID. I have often used the phrase that ID subsumes neo Darwinism and I firmly believe it because without neo Darwinism life would be very limited and stilted on this planet. People who support ID go immediately to what many neo Darwinists claim about the ability of this process to produce all the changes in biological organisms and then trash the whole theory. That is not good science. That is not logical. That is foolishness. I believe we should add a term to the concepts we use and that is "devolution" and point out that devolution is also part of the life change process and its main engine is neo Darwinism. While the term devolution usually carries a negative connotation, not all devolution is negative. We have had peripheral discussion over the last two years about where does all the variation come from in a population. It is something that neo Darwinism would not predict because the processes of neo Darwinism tend to remove variation from a population. Of course the obligatory response by those who support gradualism is that mutations are the source for this variation but what the Edge of Evolution has shown is that is highly unlikely. I remember great_ape saying that this was a problem for gradualism or naturalistic evolution. The genetic side of neo Darwinism causes population variation to decline. And while Sanford's book argues that this will eventually lead to extinction of a species, new species constantly appear suddenly in life's history and presumably the new populations appear with lots of variation because they seem to radiate out into many sub-species. And this is where neo Darwinism is essential for survival because given all the new variation, natural selection allows the species to survive in many different environments. In other words it allows sub variants to blossom where if not for neo Darwinism the species might go extinct sooner in the new environment. In other words the built in variation and neo Darwinism allow life to flourish, But we have not built a taxonomy that goes up as gradualist claim but a taxonomy that goes down to finer and finer variations of the original population. And to me this fits ID to a "T." So I suggest we embrace neo Darwinism, argue against gradualism especially the Blind Watchmaker Thesis but point out how neo Darwinism helps make life flourish in many cirucmstances. I already above have made the point that neo Darwinism is essential for modern medicine. If one wants to go over again how that discussion started, read Seekandfind's comment at #40 where he points out that the perception is that those who believe in ID are backward and a hindrance to science and that this hurdle has to be overcome. One way to overcome this is to embrace neo Darwinism and it devolution effects, some of which are good and some of which are bad for life. In evolution some are good and some are bad; in medicine nearly 100% are bad.jerry_{December 9, 2007
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Hi I've been a lurker for while, and enjoy the banter and useful information regarding the ID/neo-Darwin/Creation debacle. Has anyone proposed a research project that is ID friendly or is anyone busy in such a project? I am interested. Also, here a possible proposal for such a project that might turn out to be useful, not only in the ID/non-ID debate but also with practical implications. http://telic-meme.blogspot.com/2007/12/epigenetic-control-of-transversion-and.html Any thoughts? Thank youTelic-meme_{December 9, 2007
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Classical NDE is envoked to explain the origin of new traits by very small changes over long periods of time. The changes occur by mutation of existing DNA and the resulting changes in proteins, processes and structures. Lateral gene transfer supplies material for change but it does not come from neodarwinian processes. It is simply borrowed from another organism. Explaining the origin of the genes that are transfered in is another question.
idnet.com.au, I think you misrepresent NDE. THere is nothing in NDE is mandates changes in organisms to either take long or to be small. Nobody looks, for example, at drug resistance in bacteria and claims this runs counter to NDE. And that certainly is a fast process. Likewise, nobody looks at horizontal gene transfer and claims it runs counter to NDE. If I'm wrong, could you point me to an actual reason why HGT runs counter to NDE. What would make it run counter would be if it could be shown that the HGT was pre-planned to achieve a certain goal and not a randomly occurring process.
Flagellar proteins are interesting. We should see some mutations that are neutral in these genes.
Why would neutral mutations in flagellar proteins be interesting? Or, why would they be more interesting than any other neutral mutations. What is the actual goal in looking at neutral mutations in the first place? Do you want to use a 'molecular clock' to determine if the split between humans and baboons occurred at a certain timepoint?
It will take years to assess the data gained from the sequencing I have suggested. I think it will add to our understanding of how powerful NDE is over 3 Billion generations and whether ID is threatened by NDE.
I think you overestimate the complexity of the project. You can get the two E.coli strains for a couple of hundred bucks from strain collections (or for free from other labs). The sequencing cost for the two strains would run under $20.000. And for the analysis you can rely exclusively on the NCBI databases which are available for free. All you'd need is a personal computer and internet access. All in all, the project could be done by a single person in a few months and cost less than $50.000 (including pay for that person). But I doubt the even the DI would offer a grant to do this, unless you can actually articulate what you would hope to achieve. Judging from an NDE point of view we would expect the following results: The E.coli in baboons should differ from the E.coli in humans in the key genes that allow them to be better adapted to the different environments. Probably the main difference between the two would be the available food sources. Apart from that we would expect neutral mutations in all genes. How does this differ from the ID predictions? Secondly, why would this experiment show what "evolution (or ID for that matter) can achieve". The environment that E.coli find themselves in (be it baboon or human) to me appear to be quite constant throughout the history of the species (except for available nutritional sources). Why would we expect to see much of any change (be it from evolution or ID)? If I was an intelligent designer, I would give my baboon bacterium a few enzymes to break down the sugars baboons ingest most commonly and then sit back, relax and enjoy the show. In humans, I guess in the past 50 years or so, I would add in a few genes that confer resistance to antibiotics. Unfortunately, that is also exactly what 'evolution would do'.hrun0815_{December 8, 2007
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Exactly!! :-)tribune7_{December 8, 2007
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tribune7,
I think what we can know is that when someone posts something like this at 7:33 a.m. on a Saturday morning he has had one heck of a Friday night.
Uncommon descent = hair of the dog? :-)getawitness_{December 8, 2007
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Jerry and Joseph, Why should anyone here on this site try to make peace with the term neo-Darwinism when the term neo-Darwinism is exactly what has been fought against for so long by so many, and need I remind, with severe consequence to reputation and career? From the mountain of evidence I've seen, The whole theory (neo-Darwinism) is a blatant fallacy with no redeeming quality whatsoever, as far as foundational science is concerned, and I will not compromise by saying "Oh this one little part of neo-Darwinism is true", When in fact micro-evolution and Genetic Entropy explain what we are seeing, in the evidence, much more clearly and with a lot more explanatory power than the term neo-Darwinism does. As you stated Jerry everyone is entitled to their opinion, I respect your opinion, but I will stick to my fool's errand as you put it.bornagain77_{December 8, 2007
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Frost122585--you need to recognize dog- there could be all kinds of stuff going on in other dimentions that we dont even know about. I think what we can know is that when someone posts something like this at 7:33 a.m. on a Saturday morning he has had one heck of a Friday night.tribune7_{December 8, 2007
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Please read that I am using neo Darwinism in modern medicine not evolutionary biology. You just think you are. Mucho, mucho modern medicine is about mutations to the genome and its effect on people and what types of drugs, procedures, operations can be used to counteract the deleterious effects of these mutations. Mutations were discovered independently of the efforts of Darwin's successors to spread his theory. They were subsequently incorportated into a pre-existing theory. Had Darwin never lived mutations would still have been discovered and their deleterious effects observed in the practice of medicine.pk4_paul_{December 8, 2007
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hrun0815 Classical NDE is envoked to explain the origin of new traits by very small changes over long periods of time. The changes occur by mutation of existing DNA and the resulting changes in proteins, processes and structures. Lateral gene transfer supplies material for change but it does not come from neodarwinian processes. It is simply borrowed from another organism. Explaining the origin of the genes that are transfered in is another question. Flagellar proteins are interesting. We should see some mutations that are neutral in these genes. It will take years to assess the data gained from the sequencing I have suggested. I think it will add to our understanding of how powerful NDE is over 3 Billion generations and whether ID is threatened by NDE.idnet.com.au_{December 8, 2007
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Why don't you just read what Jerry writes instead of jumping to the wrong conclusion?Joseph_{December 8, 2007
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Jerry, A boy brings an F home for a grade in English class. The father looks at his son and says,"But son, English is the language that you speak at home." Neo-Darwinism, the primary axiom of biology as Sanford calls it, is the reigning paradigm of biology. Its common meaning in society, and especially on this very blog, is that all life arose by common descent by purely natural causes i.e. by RV/NS. You are clearly obfuscating neo-Darwinism's common meaning by saying, "Well I didn't mean neo-Darwinism in that very large sense, I meant neo-Darwinism in only this very limited, restricted, sense. That limited, very restricted, sense for neo-Darwinism is commonly called micro-evolution, especially on this blog Jerry. Dr. Behe and others are very clear, and take great pains of effort, to show that neo-Darwinism, as it is commonly understood in society, and commonly used on this very blog, is blatantly false. And Yes, they (Dr. Behe and others) do say that "micro-evolution", which has a much more specific meaning than neo-Darwinism does, does indeed occur. I can assure you that Dr. Behe, Dr. Sanford, Dr. Dembski, as well as numerous others, will, without any hesitation whatsoever, say a resounding NO! when asked the question, "Do you believe in neo-Darwinism?" So why not use the term micro-evolution instead of neo-Darwinism when that is what you really mean Jerry?bornagain77_{December 8, 2007
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bornagain77, You should read what I say. At the end of my post, I said "I never said neo Darwinism created any novelty. If you can show me where I said that it would be appreciated so I can correct it." So that should give anyone reading it a hint that I do not think neo Darwinism is the source of much of the change in biological organisms for the last 3.5 billion years. In fact on numerous occasions in the last couple years I have argued just the opposite. So there we have a starting point and any discussion should not be about evolution unless you want to argue that neo Darwinism explains a lot of evolution and then I will argue against it. Does the fact that I hold this belief mean that the theory is totally useless. The answer is no. Numerous theories are very good at certain things but not good at others. Is this hard to understand. A good example is Newton's theories of motion. A great theory for most motion we observe but breaks down when the relative motion gets very high. So where are we. I maintain that ID is completely consistent with neo Darwinism as a science and I see no problem with this if you look at just the mechanisms of neo Darwinism. Mutations do happen. ID does not deny this. These are a major concern for modern medicine. ID does not deny this. Natural selection and genetic drift do happen. ID does not deny this. Allele frequencies in population change and medical health is affected by these processes. ID does not deny this. All are easily demonstrated. All are very relevant for modern medicine. I never said it had much to do with evolutionary biology. So leave it out of the discussion. And I bet if you asked John Sanford, he would agree with each of the previous statements. I bet Behe, Dembski, Meyers and anyone else you get from the ID proponents would agree. What they disagree with is the claims many make for neo Darwinism in terms of evolutionary biology not that the mechanisms of neo Darwinism don't happen. Please read that I am using neo Darwinism in modern medicine not evolutionary biology. Mucho, mucho modern medicine is about mutations to the genome and its effect on people and what types of drugs, procedures, operations can be used to counteract the deleterious effects of these mutations. The huge growth in medicine can mainly be explained by this phenomena. Behe's book, The Edge of Evolution was essentially about mutations in microbes and how they have had a devastating effect on humans. He looked at mutations in both the microbes and humans and how natural selection played a role. That sounds like neo Darwinism to me. The main thrust of the book was not that neo Darwinism didn't work but what were its limits or the edge of change that it could produce. From what I understand Sanford's book is about natural selection and what it can do when presented with various types of mutations. That sounds like neo Darwinism to me. The issue with medicine is much different than that for evolutionary biology. Here we are dealing with negative mutations and what effect it can have on the person or population of a species. A lot of the mutations which are negative on the Kimura curve are in a selectable region. And neo Darwinism works in the negative region as well as the positive region and has deleterious effects. So neo Darwinism is not very good for the big things of evolution but it is very good for explaining a lot of the problems of modern medicine. And to deny this is foolish. An aside. I believe the best way to approach the argument about the relevance of neo Darwinism in evolution is to accept the theory and its mechanisms and then point out the real benefits are in medicine where mutations have a significant role but that in the evolution area it is mainly a complete bust with only trivial changes to point to. It is great at the negative end as an explanation and terrible at the positive end in explaining evolution. But to continually pan it is counter productive. Unfortunately it works but mainly in a negative direction.jerry_{December 8, 2007
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Jerry, I respectfully disagree with you, Here is a interesting article by Philip Skell refuting your assertion that neo-Darwinism is important to biology and medicine; Your assertion: "It gives the impression that it (neo-Daewinism) has no value but in reality it is the basis for much of modern medicine and is no threat to ID and evolution." Jerry post #43 The article; http://www.discovery.org/scripts/viewDB/index.php?command=view&id=2816 of special note from the article: " the modern form of Darwin's theory has been raised to its present high status because it's said to be the cornerstone of modern experimental biology. But is that correct? "While the great majority of biologists would probably agree with Theodosius Dobzhansky's dictum that 'nothing in biology makes sense except in the light of evolution,' most can conduct their work quite happily without particular reference to evolutionary ideas," A.S. Wilkins, editor of the journal BioEssays, wrote in 2000 "Evolution would appear to be the indispensable unifying idea and, at the same time, a highly superfluous one." I would tend to agree. Certainly, my own research with antibiotics during World War II received no guidance from insights provided by Darwinian evolution. Nor did Alexander Fleming's discovery of bacterial inhibition by penicillin. I recently asked more than 70 eminent researchers if they would have done their work differently if they had thought Darwin's theory was wrong. The responses were all the same: No. I also examined the outstanding biodiscoveries of the past century: the discovery of the double helix; the characterization of the ribosome; the mapping of genomes; research on medications and reactions; improvements in food production and sanitation; the development of new surgeries; and others. I even queried biologists working in areas where one would expect the Darwinian paradigm to have most benefited research, such as the emergence of resistance to antibiotics and pesticides. Here, as elsewhere, I found that Darwin's theory had provided no discernible guidance, but was brought in, after the breakthroughs, as an interesting narrative gloss. In the peer-reviewed literature, the word "evolution" often occurs as a sort of coda to academic papers in experimental biology. Is the term integral or superfluous to the substance of these papers? To find out, I substituted for "evolution" some other word – "Buddhism," "Aztec cosmology," or even "creationism." I found that the substitution never touched the paper's core. This did not surprise me. From my conversations with leading researchers it had became clear that modern experimental biology gains its strength from the availability of new instruments and methodologies, not from an immersion in historical biology." Jerry you stated: “ID is completely consistent with neo Darwinism as a science.” This is blatantly false! Please tell me how you reached this fallacious conclusion. (please use small words, as my reading comprehension is not as advanced as yours, as you have pointed out) You stated: An aside; explain to me what novelty genetic entropy has created. ID (Intelligent Design) creates all novel complex information (CSI). Genetic Entropy states that no new information will ever arise by natural processes and will decrease upon sub-speciation events. (I can go get a dictionary, if you want, and try to put Genetic Entropy into bigger words so you will finally be able to understand it.) Since I am having such a hard time reaching your superior intellect, and you think I'm retarded and will not listen to me, may I refer you to Dr. Sanford's book; "Genetic Entropy" (It has plenty of big words for you to chew on.) http://www.amazon.com/Genetic-Entropy-Mystery-Genome-Sanford/dp/1599190028 Book Description: "Dr. John Sanford, a retired Cornell Professor, shows in Genetic Entropy and the Mystery of the Genome that the "Primary Axiom" is false. The Primary Axiom is the foundational evolutionary premise - that life is merely the result of mutations and natural selection. In addition to showing compelling theoretical evidence that whole genomes can not evolve upward, Dr. Sanford presents strong evidence that higher genomes must in fact degenerate over time. This book strongly refutes the Darwinian concept that man is just the result of a random and pointless natural process."bornagain77_{December 8, 2007
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bornagain77, said "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." I am not making any peace at all. In fact I am being a little belligerent and trying to rid a nonsense mentality exhibited by many on this blog. Probably an impossible task since many come here with with moral certainty and blinders on about things they do not understand. As I said the reading comprehension skills are not the best on this blog of which your comment above is an exemplar. Blind knee jerk reactions describe a lot of the posts. I am merely stating the facts as I see them. By the way when did I bring up anything about the fossil record that you disagree with? I suggest you try and understand just what neo Darwinism is and can do. After all both Behe and Dembski accept it so try to understand why. The thing they say about it is that it is limited. Which is completely consistent with what I have said. There do I have to spell it out any clearer. Neo Darwinism works but it is limited and is very appropriate as a model for much of genetic diseases and because of this is very valuable in modern medicine. An aside; explain to me what novelty genetic entropy has created. I never said neo Darwinism created any novelty. If you can show me where I said that it would be appreciated so I can correct it.jerry_{December 8, 2007
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My argument against statistical analysis is from the perspective of Johannes Keplar who said it was like living in Plato’s cave- taking everything and putting it into math and worse incomplete mathematical analsys as Kurt Godel pointed out- does not describe actual reality because it is incomplete and therefore not suficient to describe "the world as we know it" -this is why those stupid computer programs where DE works are incorrect. They are essentially a human logical mind that takes subjective information and makes it horribly communicable- The real universe is out of our reach- but in our reach to investigate- this objective idealism opens up the possibility for differing modes of investigation - ways of guessing based on intuitive apriori knowledge instead of being forced to live in a cave where all we can know and think about is merely a "shadow" of the actual world. We should expect design- and prepare for it even if we cant yet predict its nature- this is the true mode of inquiry (what is possible)- not one where you know what’s going to happen and you test it but where you prepare for things the best you can and shape your view point based on its intuitive impact on you - open-minded with expectations. The shape of things to come is more important than the rules by which you must fallow to know what comes next- any rule that exists must be ignored as it only confines one's intuitive sense which is the true guider of a man's compass- Or as Einstein put it when he was talking to J D Rockefeller Rockefeller: You know Einstein to me its all about organization- I put my faith in organization... Einstein: I put mine in intuition. There was a book recently written called the deviant advantage. As the other quickly pointed out his definition of deviation was statistical not moral- but as one can see statistical deviation is almost an oxymoron- if it doesn’t fit stats how can we account for it? The book was about how all of the great ideas have come from minds which chose to deviate from the norm. But why did they do it? It was given their intuitive insights and adventurous unbridled spirit that moved those accomplishments and theories to th forefront- This is the way we should do science- this is the true way to do experimentation - this is where the real break troughs reside. This explains why we havent had the success treating degenerative diseases and th elike that we once expected would be eradicated so quickly- people's ignorance and demand for control of other people's minds have constrained expierementation in recent years- you cant get a grant unless you idea is liked- you cant get into a pristine college unless you have a 4.0 - Albert Einstein failed the liberl arts section of his college enterance exam. A statistical society is a stupid society- statistically speaking that is.Frost122585_{December 8, 2007
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To visually support my idea of how it might have happened - think about a computer- now say you we inside of the computer- one of those programs for instance - what if you knew that there was a history of the program - a computation history- you might suppose that everything was front loaded but you know that we can go into a program at any pint and alter or add information- The person inside the computer would not understand this though because to him it was all part of the unfolding process. Perhaps the computer mind in this case is a program that moves across the spectrum and while considers historicity cant differentiate between what was and what is. There is no way this computer mind short of programming it could understand that there is another world where biological entitles are controlling its fate- when the new information appears it seems to be normal but not new- I think that we maybe living in a matrix like world more complex and real though. Where injections of information can govern the way we exist and experience life- but all of this appears to be in a historical linear patter- "possibly to both the program and the designer" but only the program (us) actually exists in a relativistic universe. As far as practical application it has the philosophical advantage of oppening up doors. As far as scientific explanation it opens up the feild of statistical analysis to a relativistic corralative process- lest we forget it is quantum physics and relativity that the "establishment" has failed to reconicle- In other words things might be happening that are not statistically related but part of the greater picture which we see linearly. This view might encourage us to take the history of what we do know and predict the next unexpected change not by linear statistical analysis but by "obejective coheisive arrangemnent"- Marying the ralative to the statisitical or the specificity to to the complexity finding trends that are "objectively likely" but not mathematically supported. Kant called this intuitive transcendentalism- IMO Kant was the greatest philosophical-"scinetific" mind of all time. Even though he said euclidian geomatry was the end all be all and non-euclidian geomatry through einstein proved him worng- I am one who thinks that he expected this but merely reduced the non-euclidian to regular geomatry as a whole because he expected einstein and that it would eventually revert back as mathematics cleared up and reconciled the templet of euclid with einstein. Anyways, "my fasination with realities origins" maybe somthing to think about though-Frost122585_{December 8, 2007
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