Adding information to the genome.

His comment? Please see Message 257, Message 259, Message 263 and Message 265, none of which touched on the topic. Plus there's his history from his own thread, Has natural selection really been tested and verified? , eventually declaring that he was victorious and abandoning the discussion. I want to prevent Bolder-dash from repeating that behavior here.I can post a note to Report discussion problems here: No.2 and bring in moderator help, or we can police ourselves and get on-topic.

There is also the appearance of coherence in the area (you told me about) where proteins fold. I believe this is the "barrel shaped object" Stephen Meyer told us about where he narrated a video that can be found on various websites. You told us about the ph factors and biochemicals I never heard about. All of these factors being equal then we would expect proteins to fold the same way.There is also coherence in the 200 proteins that enable the cilium to operate and the synchronous movements these cilium appear to employ when I watch a video of an organism using cilium to move.

You seem to be using 'coherence' to describe several different and disparate phenomena. In the case of the cilium you seem to be using coherence both to mean the straightforward Irreducible Complexity argument and to describe the cellular physiological processes which cause ciliary synchronisation.This just serves to make things very confusing. Please can we try not to just make up our own terminology for things. If you want to talk about irreducible complexity then say so. If you want to talk about something else then be specific.TTFN,WK

Kaichos Man, please read the words, not what you want them to be. Being a prerequisite for new evolutionary progress, curiously, does not say that natural selection causes variations rather than allowing more to exist. In other words, this does not prove your point in the slightest, and in fact is consistent with what you have been told is being said as opposed to your erroneous interpretation. And again, this does not state that the relaxed selection causes the increase or boom in neutral variations, only that more variations are allowed to exist. Let me rearrange his statement by switching the two parts of the sentence:"(i) A population is liberated from the preexisting selective constraint. (ii) under relaxed selection There is a sudden increase or boom of neutral variations ..."Because of the relaxed constraints on the amount of variation allowed in the population, more new variations due to mutations and genetic drift survive to be passed on to following generations than was allowed under the previous selection constraints.When you relax the selection criteria for immigration there is a sudden boom of additional people immigrating. The relaxation of the selection criteria doesn't cause these people to suddenly exist out of the blue, rather it allows existing people to immigrate that didn't meet the previous selection criteria.When you open a water tap, more water passes through the tap than passed before the valve was opened. Opening the tap doesn't suddenly cause more water to exist.When you open a door, more people can pass through the door than could pass before the door was opened. Opening the door doesn't suddenly cause more people to exist.It is really, truly, a simple concept.Enjoy.

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Good Percy, we don't need the scientific method. I see your a real scientist at heart. No your right, I'm talking about information science. So did you?
The human brain is amazing. I can start talking to you in Spanish and you might have no idea what I'm talking about. But we adjust. You understand that I am trying to convey some information but you don't understand the code. Then we start talking slowly and/or use our body language. When I was a bit younger I journeyed the the Himalayas, I didn't know their language but I could communicate easily.You say that reality is information; what kind of a statement is that?You enquire: They come from a set of standards. I want to juggle a few objects, I need to conform to the language of the processor, a standard. The "shell" of the program informs the processor of the addressess where it should start loading and how much space it needs to allocate to the process.The next set of instructions juggle the first lot of objects and the additional information juggles the second.But of course we're talking about a binary machine, boring, lets talk about a machine that has a base FOUR system but also has 'fussy logic'. Yes Percy I'll attempt the argument.

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There no doubt exist natural laws, but once this fine reason of ours was corrupted, it corrupted everything. blz paskal

Hi LucyTheApe,Why are you quoting and responding in this thread to what I said in Message 399 over in the Evolving New Information thread? If you'd like to continue the discussion we were having in the other thread, the one that left off with you needing to explain how you calculated your figures, then you should respond over in that thread. I just posted this note over there: Message 400--PercyEdited by Percy, : Grammar.

Hi Kaichos Man,To try and stop the derailment of the Wright thread I am responding here where we have already been discussing Neutral Theory. Except of course that Kimura himself had elucidated one of those methods and the other was well established. As I have often repeated in this thread the open question is the balance between drift and selection, in this case whether the balance is different between evolution of the genotype and that of the phenotype. The genotpye and phenotype are not isomorphic but neither are they independent, the degree of 'gearing' between the two varies depending on what system is being studied. Looking at RNA enzymes there is a high degree of 'gearing' as their functionality directly relates to their secondary structure which is determined by the primary sequence. In proteins the connection is less close as there is degeneracy in the translation between genetic sequence and amino acid sequence. From metazoans there are many possible genetic variations which will have no discenible phenotypic effect at the larger scale and a subsequent reduction in the 'gearing' between the two. I fail to see how this example would in any way make Kimura wrong, his argument was that the vast majority of molecular/genotype level mutations were neutral and their propagation determined largely by chance, he never said that beneficial molecular mutations did not occur or that selection could not act upon the genotype. If adaptive phenotypes are fixed by selection it does indeed follow that a causative adaptive mutation at the genetic level similarly becomes fixed. Kimura had no problem with that, he merely proposed that such a course did not explain the vast majority of the genetic diversity that we see. You are wrong on both counts, deleterious mutations can indeed endure and become fixed in a population, in fact genetic drift is one of the reasons why this occurs, the random factor can overcome selection. The last part of course is the same canard you have been pushing for this entire thread under the guise of 'genomic information'. That is indeed poppycock, and it represents neither the view of Kimura nor even the adaptationists he was arguing against. Once again you treat the neutral and selective modes of evolution as mutually exclusive and arbitrarily insist only one can pertain to any given level. In actual fact there are mixtures of both neutral and selective/adaptive evolution at all levels. Nowadays Kimura's contention that the majority at the molecular level is neutral is widely accepted and while at the phenotypic level things are less clear cut, as there are still some strong adaptationists out there, the existence of mutations producing nearly neutral changes in phenotype is certainly accepted.Kimura Saying that he considered some phenotypic changes to be nearly neutral is a far cry from saying he considered all phenotypic change to be neutral or deleterious, clearly only someone with your peculiar ability to interpret Kimura's meaning could have gleaned that from anything he said. None of this is true and you have not a shred of evidence to support it. Your final quote speaks to Kimura's ignoring the place of adaptive mutations in his mathematical approach to calculating the rate of evolution, as genetic change, per generation. To take it as meaning that Kimura believed beneficial mutations did not occur is the most blatant sort of quote mining.TTFN,WK

Wounded king, Subfunctionalized Monarch, I cannot let you get away from this. I'm sick to death of pulling out quotes and farting around with HTML tags, so I will put this simple proposition to you:Given that one is simply the physical expression of the other, it is logically impossible that the genotype and the phenotype evolve by different processes.If you don't believe this is true, please provide an illustrative example of how this might happen- remembering that a selective evolution of the phenotype immediately becomes a selective evolution of the genotype.P.S. Characterising an advocate of an opposing viewpoint as a "troll" is cheap at best and paranoid at worst- but let's not get sidetracked. Answer the question.

You're repeating the same question Wounded King just answered, where he said this: I think you're going to have to break down, use some dBCodes to quote some part of WK's answer, then respond to that. Just asking the same question again isn't going to help the discussion make any progress.Note that at one point WK uses "gearing" as an analogy, and it's a good one. For example, as long as the mutations are neutral with respect to phenotype, genomic change can churn away without affecting that phenotype. It is even possible for mutations that do affect the phenotype to be neutral with respect to selection.--PercyEdited by Percy, : Minor clarification in last paragraph.

I have never said that they evolve by different processes. I have consistently maintained that the same processes pertain to both, but that the balance of drift/selection on each is different depending on precisely what one is studying as the phenotype. But a non-selective evolution of the genotype may have absolutely no effect on the phenotype which is where the disjunction between the 2 can arise allowing the balance of drift/selection to vary. I agree that amount of selection is maintained between the 2, since it is effectively the phenotype which is being selected, but the amount of neutral evolution is where the discrepancy arises.So any example where portions of the genetic sequence diverge through drift while a few bases are maintained or propagated by selection should be sufficient. Such examples are present in virtually every single comparative genetic study ever done which identified even 1 nucleotide under selection, because such studies are likely to find many sites which are not being constrained by selection.You say ... ... but you neglect the fact that there is no corresponding phenotypic expression of many neutral mutations. My entire point was that the extent to which this is true varies depending on what you are considering as the phenotype. If you consider the protein product to be the phenotype it is less true than when we consider the gross morphology to be the phenotype of interest.I don't believe it is meaningful to talk of neutral evolution of the phenotype when the phenotype has not in fact undergone any change. Would you agree with this? If so then you must concede that the rate of neutral evolution between phenotype and genotype is partially decoupled.TTFN,WK