Summations Only

But the duplicate did not exist, therefore it is novel sequence. And yet here we have just such a sequence occuring through random mutations. It is a series of DNA sequence changes that result in a trait that the bacteria did not have before these changes occurred.

Hi zaius,I gave your post a cheer because you actually did present some evidence for your claim. However, I don't think you have made a very strong case.Here is a link to the full text version of the paper you cited: Genomic analysis of a key innovation in an experimental Escherichia coli population (Its helpful to have more than just the abstract)The very first line of the article gives a clear definition of novel features.

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Evolutionary novelties are qualitatively new traits that open up ecological opportunities and thereby promote diversification.

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The authors then go on to explain how the process is thought to give rise to these novel functions.

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These traits are thought to arise typically by the exaptation of genes that previously encoded other functions through processes such as domain shuffling, altered regulation and duplication followed by neo-functionalization. Multiple mutations may be necessary to produce the new function, and thus its potential to evolve may be contingent on subtle differences between species, populations or even genotypes.

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It is important to note that this is not just a case of duplicate an existing gene and go, but it involves multiple steps in the development of the feature. The authors refer to three steps in the evolution of this trait; actualization, potentiation and refinement. The Cit+ variant first appeared at 31,500 generations, but was very weak. But before that duplication could even be expressed, there needed to be a genetic background that allowed the new trait to function. And then the trait needed to be refined by subsequent mutations in order to be efficient.

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The evolution of citrate use also highlights that such actualizing mutations are only part of the process by which novelties arise. Before a new function can arise, it may be essential for a lineage to evolve a potentiating genetic background that allows the actualizing mutation to occur or the new function to be expressed. Finally, novel functions often emerge in rudimentary forms that must be refined to exploit the ecological opportunities. This three-step processin which potentiation makes a trait possible, actualization makes the trait manifest, and refinement makes it effectiveis probably typical of many new functions.

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SO these are the reasons that people that have done the research on this are calling it "novel." You can dismiss it as not being novel if you choose, but it really misses the point altogether. This is not an instance of the cell deciding it needed to be able to utilize citrate and simply duplicated its "pre-existing" components. How can you even make this claim? How do you know it has never been "pruned" by evolution? You are really stretching the facts far beyond what you actually know. How so? This is simply jumping to a conclusion and avoids the issue at hand. Why is this not a novel trait? Even if it was "front-loaded", it still meets the definition of novel. The trait was not there before and now it is and it promotes diversity and exploitation of a new ecological opportunity. It is not simply a case of turning a switch on, it is a whole series of changes that result in something new; or in other words ... novel.HBD

(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.

And that, my friend, is as good a definition of the process of evolution at you're ever likely to get.

Hi Zaius,I have the same reaction as Tangle. You appear to agree that evolution produces the types of features everyone else describes as novel, you just won't accept that term yourself.--Percy

That was a feature it did not have before which makes this feature novel.To use an analogy, you would not call the evolution of lungs novel. Why? Fish could already utilize oxygen in an aquatic environment. Fish evolving legs? Nope, not novel. Fish already had limbs and had locomotion in an aquatic environment. Using your definition of novel, if we started with a very simple replicator and watched life evolve into what we see today you would not define a single one of those evolved features novel. No novel features needed to evolve anywhere in the history of life in order to get the biodiversity we see today, according to your definition of novel. What more is needed in order to produce novel features? The differences between any two species is due to SNP's, indels, and recombination events. But it does have a relevant mutations in the promoter which lead to a feature that was not present in the bacteria before the mutations occurred.Why can't novel features evolve through changes in promoter sequences? There is an entire field of biology called Evolutionary Developmental Biology that argues that DNA regulation is a major factor in evolving novel features. Then novel features evolve by evolving new keys. What is wrong with that? You have never heard of neutral drift? Evidence please. Are you really unaware that deletions occur regularly? Also, there are some species out there with very massive genomes. For example, a species of amoeba has a 670 billion base genome, 100 times larger than our own.I would also be curious to see the energy budget used to produce DNA in multicellular organisms. I'm not sure, but I think it would be pretty miniscule compared to muscle contractions and other processes. I would also suspect that speed of replication is a stronger selective force in bacteria than energy budgets for genome size.

But its absurd. By your same logic there can never be any novel ideas written down because they're just going to be combinations of pre-existing words and letters and never de-novo. As I said in Message 218:

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Think of it this way: There's only 27 letters in the alphabet. All words are just going to be combinations of those pre-existing letter. No new letters come about so according to the Creation mindset; no new information can ever be created. A new book comming out tomorrow with totally novel ideas cannot be considered new information, according to the Creation mindset, because its just using already existing words and letters so no new information is really created.

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But that's bullshit. Of course new information can come out by combining pre-existing words and letters to form new ideas. Just like new information can come about from mutations to DNA that re-arrange the ATCG's into new combinations.

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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.

Hmmm. Sure looks like some new information to me:

Exactly. I came to the same conclusion when I posed my example of a land mammal becoming "adapted" to the sea. Zaius137's response was simply that such adaptation had never happened.Is intelligence novel? Well, chimpanzees have some level of intelligence, so nothing novel about mere changes in processes that provide man's intelligence and thus there is no barrier to chimpanzees and men having had a common ancestor. Wait, says the creationist, that never happened, so if necessary I will concede that change to be novel. In fact I insist on it.From a different message:

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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. One chunk encoded a protein to get citrate into the cell, and the other chunk caused that protein to be expressed."

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Yes. That would constitute novelty under any reasonable definition. It is sufficient that novelty apply to changes in the genome that would provide support the theory of evolution from a common ancestor. If none of those changes meet the zaius137 definition, of what relevance is that?Zaius has defined novelty and 'new information in the genome' in such a way as to make any directly observed evidence for those things impossible. I am sure that even Zaius would agree that the evolution of a primate from the common ancestor of all life involves novelty, but he would require direct observation, and not the evidence that we do have, before he would consider any such thing.His second strategy is to insist that we may not consider the time involved. He calls this magic. Let me suggest that it is further evidence that Zaius137 arguments should not be taken seriously, unless your goal is to convince zaius137.What is possible is to observe a few cases of novelty that involve small changes under limit periods of observation time (i.e. within a human lifetime). It is only belief, supported by nothing else, and an unwillingness to accept anything except direct observation as evidence, that allows speculating about some barrier to direct novelty. A barrier that is neither directly or indirectly evidenced. But a barrier that for a creationist considering the citrate experiment, must be there.I would take zaius137's position in this thread as statements of what would be required for zaius137 to be convinced that the theory evolution had a scientific basis. But even those things would not convince him that the theory of evolution is correct. No evidence can do that.

You're right, that if its completely random then you won't get much. But the Theory of Evolution doesn't describe it as being completely random, there is a selective pressure too.So, in this case, it be like throwing a handful of Scrabble tiles on the floor and then selecting the groups of tiles that did happen to make words, pickinging up the rest of the tiles that didn't, and then throwing them back out again, selecting the groups of tiles that did happen to make words, pickinging up the rest of the tiles that didn't, and then throwing them back out again, and so on.Soon enough, you'll have yourself some words that have been randomly generated from the tiles. You see, though, its not completely random because you have that selective pressure. Any time a mutation adds anything to the genome it is truly new information. Just like you can rearrange existing words to form new ideas, a rearrangement of existing genomic information is the origination of new information in the genome.In the case of the E. coli, that one section of the genome was copied and pasted, and it resulted in an whole novel ability for the species. Again, with this logic, nobody can ever write down a novel idea because they're just using existing words. But we know that's bullshit.

In the case of the E. coli, you get aerobic citrate utilization which it did not have before. If that is not new information, then what is? A rearrangement is a new arrangement, and since it didn't exist before it would also be novel. The sequence needed to utilize citrate in aerobic conditions did NOT exist before, otherwise the bacteria would have utilized citrate in aerobic conditions. They didn't. It took a new arrangement of nucleotides to get a new phenotype. New functionality is new information.

It was the entirety of your message that gave me the same impression as Tangle, and I've said much the same thing in other messages. Your objections take the form of these assertions:

1. If evolution produced something, it isn't novel and it isn't new information.
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2. If something is novel and possesses new information, evolution could not have produced it.

But the evidence doesn't support these assertions, explaining why all you do is repeat them.Could you at least provide an example of a feature you consider novel before this thread closes for summations? There's no time to make any progress in this thread, but it might help begin a new thread.--Percy

This much you must admit to surely:
1.There are DNA changes.
2.They are caused by mutation.
3.They allow the modified organism to survive and replcate in an environment that would have otherwise killed it.How big a step is it for you to get to:4. This is what biologist call evolution?