Summations Only

The Catholic Scientist A novel adaptation would have to include an entire population where that population becomes homozygous to that trait. An individual organism variation would not constitute a novel trait, in other words that trait must be fixed in a population and homozygous to all individuals with new trait substituting into the original genome of the species. That is the heterozygosity completely being cleansed in the resulting genome (a classic sweep in evolution).Can a real biologist chime in.Edited by zaius137, : A clear misspeak

To the Catholic Scientist, but it is shaped as a general reply to several participants.I believe I have more than met the request made that I define what I believe is a novel innovation of a new trait or novel Phenotypic Variation.Concerning the E. coli exampleBy definition, I showed that the transport of citrate trough the cell wall of E. coli was not a novel innovation because under anaerobic conditions it could already take place. Point of fact concerning the definition of novel

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1) new and not resembling something formerly known or used

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This is because the transport of citrate through the cell wall under anaerobic conditions was adapted to aerobic conditions via a newly promoted recessive gene. The transport of citrate already occurred but was enhanced (adapted), in that strict sense the qualification of resembling was satisfied.Now was there a novel transporter mechanism in the genome that suddenly appeared. The answer is no. The transport of citrate in aerobic conditions (Cit+) appeared because of a tandem duplication that acted as an aerobic promoter of a previous silent transporter.

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The Cit+ trait originated in one clade by a tandem duplication that captured an aerobically expressed promoter for the expression of a previously silent citrate transporter. Genomic analysis of a key innovation in an experimental Escherichia coli population | Nature

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It is noteworthy that this silent transporter was in the genome all along never being pruned by evolution. If you can explain this please do.Rather than being an example of evolution producing a new and novel trait this research only shows that there is front loading of adaptation in the genome. A genome designed by a all powerful Creator.

(herebedragons)Since I have shown that E. coli using citrate is not a new novel trait, I would like to address the polar bear. Something bothers me hereCan selective pressure cause an evolutionary like change? In the case of bears, apparently it does not, so you rightly label it as adaptation. In fact, scientific experiments have come to the same conclusions; particularly in fruit flies. Massive selective pressure has only produced adaptation (not new novel traits). In all cases, there is a limit to adaptation; in other words, there is a limit to phylogenic change in a species that never really produces a truly novel trait. Adaptation is always a better definition, as you seem to verify.Interesting that Polar Bears and Grizzlies can and do interbreed (Pizzlys). Supposedly, the two groups diverged about 5 million years ago, about the same time as the chimp human divergence. There is an extraordinary environmental pressure rift between the two bears yet they remain bears. Awkwardly the environmental pressure on pre-human hominids is not as well defined as in bears. In one case, you call natural selection as a force for adaptation in bears but what about human evolution.Is there a consistent expectation in the theory of evolution or is it on a case-by-case basis. If the latter is true, do you have a theory or just a philosophy? You did not mention the classic sweep (an important omission).I do not think you have a grasp on what I am actually claiming. For the record:There is no evolution, only adaptation. Therefore, when you say, you have it completely backwards I say to you that you miss the point. I addressed this in a previous post Heterozygous in terms of per capita I will let you figure that one out.

Percy, The definition you can use does not exist. Fins evolving into legs are complete and utter fantasy. Now you need to make scientific arguments that support your speculation. The science is clearly on my side while wild speculation seems to be your only arguments.

Tangle, I am not ruling out changes, but to what degree and the mechanism for them. As to the last part of the preceding sentence, science still lacks understanding.Maybe my drift of this post is possibly all wrong. I thought there might be two sides to a debate. I am not contributing to the evolution view of new novel traits; although there are scientific arguments to make, (P.S. I have not found one that is convincing to me). Do you want me to debate myself? Seems a bit psychotic.Now lets talk evidence.

Taq,By strict definition, the trait is not novel. Sorry, genes not expressed, not promoted, silent.Yes, the new phenotype came about by mutations Your point is. True, it was adapted to an aerobic condition. The expression of that trait was silent it was promoted by a mutation. Please point out your interpretation of the following quotation.

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The Cit+ trait originated in one clade by a tandem duplication that captured an aerobically expressed promoter for the expression of a previously silent citrate transporter. Genomic analysis of a key innovation in an experimental Escherichia coli population | Nature

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Your point is that we differ from the apes. I might answer yes and claim common descent is not scientifically viable.

Taq, The sequence that tandem duplicated did exist beforehand and the Cit+ was promoted by that duplication. That is why Lenski said a previously silent transporter. Cit+ was already present in the three clades described in his experiment; the Cit+ promoter was captured by that duplication event. As I have stated before, long coding Sequences never appear by random chance. The difficulty exposed by probability opposes such a suggestion.The Cit+ trait originated in one clade by a tandem duplication that captured an aerobically expressed promoter for the expression of a previously silent citrate transporter.

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"It wasn’t a typical mutation at all, where just one base-pair, one letter, in the genome is changed, he said. Instead, part of the genome was copied so that two chunks of DNA were stitched together in a new way.

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A quote from the Wiki:

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Major genome duplication events can be quite common. Gene duplication - Wikipedia

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I have no idea why Lenski would pose such a prevarication.

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One chunk encoded a protein to get citrate into the cell, and the other chunk caused that protein to be expressed."
http://news.msu.edu/.../evolution-is-as-complicated-as-1-2-3

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Looks like a single mutation event to me.

Malcolm.Wonderful and thoughtful response my friend. You and your like are the entire reason I attend these forums. I see your point. The tip at which I believe such a yardstick could be used would be when a population actually fixed a beneficial mutation. At that juncture, if SNP mutations were identified you might ask is there a tendency to reduce heterozygosity to zero at the SNPs flanking the selected site (indications of a classic sweep). So far, there has been no positive evidence I have run across. If there ever turned up such a case and it was unequivocal, it would strengthen the evolution argument immensely. Why I believe the evidence for a classic sweep in this case of E. coli is not likely, is because the findings in studies of fitness seem to level off in a consistent manor that parallels other observations of other organisms; not precluding sexual reproducing populations. Why I even attempt such a comparison is that there seems to be a limit to adaptive changes. The sexually reproducing populations face further challenges in beneficial mutational fixation adding to the uncertainty that a classic sweep is possible. In addition, I hope given the well-documented genome and well-known homology of E. coli variances you are very successful in identifying it. Of course, you must answer yes. The entire matter of how a gene accomplices what it does is a matter of much investigation. This is where a programming background may yield some useful insight. As a programmer, I often used controlled random number generators to produce and enhance useful output. Take for example a learning program or a game. Now if these random numbers showed up in the wrong place the consequences would be disastrous. I view somatic hypermutation as a clear example of the use of controlled mutation and a similar mechanism should not be discounted as a possible mechanism in adaptation. I see the example you quoted and there is a lot going here In the case of digit placement and organization I can not see how you could claim that anything except massive changes to hox gene would work in defining a change from a fin to a hand. I still must refer to the newly discovered larger organization of the hox gene in determining things like digit morphological identity.

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When the Hox code of the of the anlage of the chicken hind limb digit I is altered to match that of digit II, the resulting foot has two similar toes both resembling digit II in morphology. This suggests that the misexpressed gene, Hox-4.6, plays a role in controlling digit morphological identity. Other phenotypes observed in the proximal parts of the hind limb and in similar experiments in the wing also lend support to this interpretation. The role of Hox genes in limb development - PubMed

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About a fin turning into a hand. I should say that all observable evidence says it is scientifically impossible. Given the experiments with E. coli and Fruit flies there is just not enough change in the genome to produce a comparative event. As I have gone threw before and I know I will probably get chastised for it New structures require new information they do not arise from SNPs. Small adaptive changes do not a limb make. I really would like to talk about this one but it defiantly does not fit into this thread. Let us see if we can maybe migrate to another applicable post. I gave the biblical accountIf you supplied an intense selective pressure to a sexually reproducing long generation organism there is not going to be a rapid fixation of this trait I imply the 630k year time frame parallel between humans and E. coli is insufficient.

(herebedragons),Thank you for the full citation great stuff, prompting further thought. I think that I explained my position about novelty. The process of utilizing citrate was already at play in this organism under anaerobic conditions. A series of mutations allowed the adaptation of moving citrate threw the cell wall into the cell under aerobic conditions. The process was well known but the implementation was adaptive to improve a inept existing function not novel.It is important to note that the authors speak from a preconceived notion that evolution is in fact the only mechanism that exists in biology. Mutations never provided more that a few SNP’s and a duplication for this adaptation. It is the same error that evolutionists have always made; their conclusions out stretch the evidence. One can ask how the coding for the protein (citT) was there in the first place.My basic argument still remains intact evolution never add de-novo sequences. Potentiating comes before actualization my friend. The problem is this so-called novel mechanism centers on the effective activation of the promoter and has no relevant mutation in the citT sequence. Activation was the novel addition here. This is like having a car without an actual key, but you are trying multiple perturbations of key cuts that might start it. Some keys do not turn as easily as others do, but eventually you find one and it starts the car easily. The evolutionist calls this a novel key; the Creationist calls this an adapted key. The car was already there, the key was not.The authors have invented a three-step process to new functionality. Multiple steps to adaptation does not help the case for an evolution process producing a new novel trait. On the contrary, why mutations that did not provide any immediate benefit were even fixed in a population at all. The authors claimed that precursor mutations (about 2) built up sometime after generation 20,000 and fixed in the entire clad of that genome. Furthermore the Cit+ coding that actually provided the protein was silent in the genome. Again where did it come from?I say the rub is how these potentiating mutations are preserved as an intermediate non-functional appendage in the genome. Why? Not at all, it is a case of an adaptive machine that was designed to take advantage of random mutations to maintain survival. If evolution is true, there must be mechanisms for pruning a genome or else it would become untenably large by preserving unneeded or outdated sequences. There is an energy cost to reproducing gene strings and you might think that it becomes deleterious to reproduce junk DNA.

Your wordsOf course new information can come out by combining pre-existing words and letters to form new ideas.Not unless you form the sentences and coordinate a thought.Try just dropping a continuous string of letters together by random or for that matter, drop a string of random words together. What new information did you get?This is where it comes together my friends. Science has never seen a spontaneous assemblage of strings of nucleotides to form meaningful information. There is always a source of existing information rearranged to produce a new adaptation or an intelligent intervention to rearrange those segments.Give me one example of truly new information being originated in the genome, it is simply a rearrangement of existing information. Case in point is the citT segment. It existed in the preceding generations but was not promoted. The E. coli adapted to a new food source by a promotion of existing information.SNP’s and inversions do not make new information. They simply rearrange or disrupt the existing background for adaptation to new functionality.If you have a single example of spontaneous entropy decrease now is the time to present it.

Unfortunately Tangle did not quote my entire paragraph context is important sometimes. I can only agree on the results of the investigation and not the conclusions.

(herebedragons) Sorry but not a living soul on this planet can explain it scientifically. I will counter with adaptation uses existing materials to develop new features and new functions for existing features. But adaptation will never change one species into another. Adaptation is observed, evolution has never been observed. My point is scientific yours is speculation.The question begging an answer is where the "features" that existed beforehand came from if not from a creator. Now explain how citT evolved and speculate all you need to. It not only doesn’t but it cannot. Your ongoing strategy of compartmentalize and concur. Since evolution is speculation, you must replace it with adaptation. Unless we are talking about religion or philosophy. I am flattered, but really, I am not that clever. You are losing the debate because you are simply in the wrong. Try using the word of God to navigate science and you will enjoy the same rate of success I do.