|
Register | Sign In |
|
QuickSearch
EvC Forum active members: 65 (9164 total) |
| |
ChatGPT | |
Total: 916,908 Year: 4,165/9,624 Month: 1,036/974 Week: 363/286 Day: 6/13 Hour: 1/2 |
Thread ▼ Details |
|
Thread Info
|
|
|
Author | Topic: How novel features evolve #2 | |||||||||||||||||||||||||||||||||||||||
Taq Member Posts: 10085 Joined: Member Rating: 5.1
|
The sequence that tandem duplicated did exist beforehand and the Cit+ was promoted by that duplication. But the duplicate did not exist, therefore it is novel sequence.
As I have stated before, long coding Sequences never appear by random chance. 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.
|
|||||||||||||||||||||||||||||||||||||||
herebedragons Member (Idle past 887 days) Posts: 1517 From: Michigan Joined:
|
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.
quote: The authors then go on to explain how the process is thought to give rise to these novel functions.
quote: 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.
quote: 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.
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. 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.
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. 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. HBDWhoever calls me ignorant shares my own opinion. Sorrowfully and tacitly I recognize my ignorance, when I consider how much I lack of what my mind in its craving for knowledge is sighing for. But until the end of the present exile has come and terminated this our imperfection by which "we know in part," I console myself with the consideration that this belongs to our common nature. - Francesco Petrarca "Nothing is easier than to persuade people who want to be persuaded and already believe." - another Petrarca gem.
|
|||||||||||||||||||||||||||||||||||||||
zaius137 Member (Idle past 3439 days) Posts: 407 Joined: |
(herebedragons),
Thank you for the full citation great stuff, prompting further thought.
The authors then go on to explain how the process is thought to give rise to these novel functions. 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.
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. 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?
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. Not at all, it is a case of an adaptive machine that was designed to take advantage of random mutations to maintain survival.
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. 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.
|
|||||||||||||||||||||||||||||||||||||||
Tangle Member Posts: 9516 From: UK Joined: Member Rating: 4.8
|
zaius writes: A series of mutations allowed the adaptation of moving citrate threw the cell wall into the cell under aerobic conditions. And that, my friend, is as good a definition of the process of evolution at you're ever likely to get.Life, don't talk to me about life - Marvin the Paranoid Android
|
|||||||||||||||||||||||||||||||||||||||
Percy Member Posts: 22505 From: New Hampshire Joined: Member Rating: 4.9 |
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
|
|||||||||||||||||||||||||||||||||||||||
Taq Member Posts: 10085 Joined: Member Rating: 5.1
|
A series of mutations allowed the adaptation of moving citrate threw the cell wall into the cell under aerobic conditions. 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.
Mutations never provided more that a few SNP’s and a duplication for this adaptation. 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.
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. 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.
The evolutionist calls this a novel key; the Creationist calls this an adapted key. The car was already there, the key was not. Then novel features evolve by evolving new keys. What is wrong with that?
I say the rub is how these potentiating mutations are preserved as an intermediate non-functional appendage in the genome. Why? You have never heard of neutral drift?
Not at all, it is a case of an adaptive machine that was designed to take advantage of random mutations to maintain survival. Evidence please.
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. 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.
|
|||||||||||||||||||||||||||||||||||||||
New Cat's Eye Inactive Member
|
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. 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:
quote:
|
|||||||||||||||||||||||||||||||||||||||
zaius137 Member (Idle past 3439 days) Posts: 407 Joined: |
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. Your words Of 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.
|
|||||||||||||||||||||||||||||||||||||||
zaius137 Member (Idle past 3439 days) Posts: 407 Joined: |
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 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.
|
|||||||||||||||||||||||||||||||||||||||
Coyote Member (Idle past 2136 days) Posts: 6117 Joined: |
Give me one example of truly new information being originated in the genome, it is simply a rearrangement of existing information. Hmmm. Sure looks like some new information to me:
Religious belief does not constitute scientific evidence, nor does it convey scientific knowledge.
|
|||||||||||||||||||||||||||||||||||||||
NoNukes Inactive Member
|
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. 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:
quote: 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.Under a government which imprisons any unjustly, the true place for a just man is also in prison. Thoreau: Civil Disobedience (1846) The apathy of the people is enough to make every statue leap from its pedestal and hasten the resurrection of the dead. William Lloyd Garrison. Well, you may still have time to register to vote. Even North Carolinians can still register for early voting. State Registration Deadlines
|
|||||||||||||||||||||||||||||||||||||||
New Cat's Eye Inactive Member
|
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? 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.
Give me one example of truly new information being originated in the genome, it is simply a rearrangement of existing information. 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.
SNP’s and inversions do not make new information. They simply rearrange or disrupt the existing background for adaptation to new functionality. 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.
|
|||||||||||||||||||||||||||||||||||||||
Taq Member Posts: 10085 Joined: Member Rating: 5.1
|
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?
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?
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. 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.
SNP’s and inversions do not make new information. They simply rearrange or disrupt the existing background for adaptation to new functionality. New functionality is new information.
|
|||||||||||||||||||||||||||||||||||||||
Percy Member Posts: 22505 From: New Hampshire Joined: Member Rating: 4.9
|
zaius137 writes: 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. 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:
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
|
|||||||||||||||||||||||||||||||||||||||
Tangle Member Posts: 9516 From: UK Joined: Member Rating: 4.8
|
zaius writes: 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. 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?Life, don't talk to me about life - Marvin the Paranoid Android
|
|
|
Do Nothing Button
Copyright 2001-2023 by EvC Forum, All Rights Reserved
Version 4.2
Innovative software from Qwixotic © 2024