Natural Limitation to Evolutionary Processes (2/14/05)

This may well be the case in the wild but it is possible to perform similar selection for antibiotic resistance artificially on a population grown from a single bacterium which is known not to have antibiotic resistance. Fora an example see... It also depends upon what definition of evolution you are working under, if you are simply thinking in terms of changes in allelic frequency then selection on 'pre-existent'variation is a perfectly legitimate example of evolution. You are obviously thinking of evolution as something generating novelty, but even with that point of view the experimental evidence shows that antibiotic resistance can arise as a novel mutation in a non-resistant population.What is very important is not to make the mistaken assumption that this is neccessarily being put forward as a response to the antibiotic. Even in the experiment I referenced the antibiotic is added after the single progenitor has expanded over many generations, to introduce variation to the population, before the antibiotic is introduced. Depending on the type of antibiotic it is certainly not impossible for resistance to arise de-novo in the presence of the antibiotic, but such a demonstration is not required to show evolution in action. This is a tricksy statement, from an evolutionary perspective simply using DNA as its genetic material is sufficient to produce the 'genetic capacity' for poison no matter what the species.TTFN,WK

I can't see the sense in this. Any decrease in frequency of one allele is going to be balanced by an increase in frequency of another allele.TTFN,WK

As I see it the problem here is your use of terms such as 'capacity' and 'possibilities'. In terms of extant allelic variation you are correct that much of the time selection leads to a restriction of variation even to the point of fixation. The problem is that in terms of capacity and possibility there is no restriction, the genes are still perfectly capable of producing any possible allelic variation as a result of mutation.In terms of producing novelty mutation, in a relatively broad sense, pretty much is everything. This depends very much on the initial prevalence of the selected trait, if the selection is very strong and the trait at very low abundance then you may see a drastic reduction in population and genetic variability, if on the other hand the selected trait is already fairly evenly distributed then there is a good chance that much of the genetic variability of the population can be maintained, except for at the particular locus under selection.TTFN,WK

Mutation is a general term for a heritable change, most mutations in terms of evolution and genetics are thought of in terms of changes to the DNA sequence, either within the primary sequence (A,C,G and Ts) or in terms of the location of sequences or even large scale rearrangements of the chromosomes up to complete genome duplications.There are also some more recently studied examples of heritable traits which are not connected to the primary DNA sequence, but these are peripheral to the question you are considering.So for our purposes a mutation is an alteration in DNA from a simple single base substitution up to large scale chromosomal rearrangement. The causes of mutation are also many and varied, some are mere mistakes in the normal replication process, others are the result of environmental factors such as mutagenic chemicals, UV light or radiation. This isn't neccessarily the case, there are some forms of selection which act to maintain diversity in a population. Some traits work best in a heterogeneous population or when they only represent a particular proportion of the population, in which case selection can maintain the frequencies of different alleles.You don't really seem to be very familiar with the basics of molecular genetics, population genetics or evolutionary mechanisms. Here is a section from a genetics textbook covering the origin of variability in mutation and the effect of selective mechanism on reducing variability.TTFN,WKThis message has been edited by Wounded King, 02-16-2005 09:12 AM

That didn't explain it better at all, it explained it exactly the same and made the same mistake again. There is no 'evolutionary' scale except perhaps in purely temporal terms. There are measures by which man could be seen to be 'top species' but there are equally many by which he is not. Do you mean what will man evolve into?TTFN,WK

Similarly mutations in related genes have produced more muscular phenotypes in mice and cows (McPherron et al., 1997).Of course Faith might argue that the father, who was not identified, harboured a defective copy of the myostatin gene, so we stll have no de novo mutation observed. Or she might pull off the old bait and switch and point out that the fact that the mutation disables what we consider the normal function of myostatin fits in exactly with her genetic degredation model of evolution.Of course all this is completely beside the point as Faith's conception of beneficial, and possibly even detrimental, is completely unrelated to evolution.There is essentially no effective way to gauge the beneficial properties of any de novo identified human mutation without tracking it through a population over several generations and even then it would be a monumental task to control it in any meaningful way.TTFN,WK

I'm not sure there is any reason to expect this to be true. You would have to know that beneficial or detrimental mutations were equiprobable and I really can't see any way, other than perhaps pure guesswork, for you to have made this calculation and come to this conclusion.TTFN,WK

I'm not sure if you meant domestic animal breeding here, but if so it seems like an odd example to use since the traits selected for domestication are often not beneficial for the animal in any context except that of fitness in the evolutionary terms you hoped to avoid since that trait causes the breeder to force an unnaturally high rate of reproduction for individuals with that trait regardless of its effects on their health or goodness for anything other than the breeders idealised 'fit'. It also seems a bad example given the high rates of occurence of traits detrimental to the animals health in many cases of such intensive breeding programs.TTFN,WK

How exactly is it an unreasonable assumption? They assume that because the child has 2 mutated copies of myostatin one may be a de novo mutation. The only reason this is an assumption is becase the child's father was not identified. A random sample of several hundred subjects showed no others bearing similar myostatin mutations. This variant is obviously quite rare, it is possible that the father also had a mutated myostatin gene but it is also possible that the mutation arose de novo. There is plentiful evidence of the existence of the phenomenon of genetic mutation so it is by no means unreasonable for this to have occurred in this case. There is absolutely no evidence for an ancestral population of only about 8 people could account for all of the genetic diversity we see extant today.One is a reasonable assumption, the other is simply fanciful. Not all assumptions are equal.TTFN,WK

I believe the gene you are thinking of in this case is called Callipyge.TTFN,WK

Once again you just make up an ad hoc, totally irrelevant explanation with absolutely nothing to support it. Did you look at any of the actual research on Callipyge before coming up with your explanation?In this case the founder of the line, the ram 'Solid Gold', is known and has been genotyped as being mosaic for the Callipyge mutation, meaning that only some of his cells carried the mutation. This mosaicism, both in the somatic and germ line, makes it virtually certain, in the absence of some previously unknown mechanism, that the mutation originated during the embryonic development of 'Solid Gold'. The specifc mutation for 'Callipyge' is not actually within a protein coding gene at all, so it in no way 'damages' or 'breaks' any gene. What the mutation, a single nucleotide substitution (Smit et al., 2003), actually does is prevent the methylation of a number of genes around it causing them to be expressed post-natally (Murphy etal., 2006).There are also no readily apparent downsides to the Callipyge allele. While there is a minute reduction in the ovulation rate it has no significant effect on conception rates, fecundity, maternal ability, or ewe longevity (Freking and Leymaster, 2006).Interestingly homozygotes for the Callipyge allele do not have the Callipyge phenotype. I haven't finished reading the paper which has a model explaining this anomaly, I might update this post when I have.I really think you need more than wishful thinking to explain this one away Faith.TTFN,WK

In what way is this not precisely 'trying to explain it away' given that it was given specifically as an example of a de novo mutation.De novo is the relevant biological term rather than novel since a mutation need not be singularly unique to have been newly generated in any particular instance.You seem now to be shifting to claiming that unless a mutation can be shown to have never arisen before then it can't be considered, which is clearly a completely impossible thing to show and is also completely irrelevant.These things are only predictable stochastically. It isn't like predicting the flight of a projectile but like predicting the behaviour of particles in Brownian motion. Can you show where you have been given a specific claim for their abundance and it has fallen flat. Other than Parasomnium's quickly retracted guesstimate I can't bring one to mind. Perhaps you just mean that they have failed to convince you. Thats perfectly reasonable, and some of the research isn't freely available anyway, but given your complete unfamiliatrity with the research might it not be a better idea to withhold comment in favour of asking questions to increase your understanding until you have comprehended the Reader's Digest version rather than going off half cocked with your own wild guesses?TTFN,WK

I'm not sure how we can be on post 284 of a thread more than a year old and you still seem to have no more idea what you are talking about vis a vis mutations than you did with message 1. As you say, you are biased towards constructing insane and impossible requirements. How can you possibly prove that a mutation has never arisen before without having the complete genomes of every animal that ever lived? And what possible relevance would this have to whether evolution occurs or not? What you have just said, bar the 'designed-in' part, is almost exactly what random mutation and natural selection is. But as I pointed out the mutations are only predictable in a stochastic manner.the arising of truly novel traits or structures would need to be based upon the compounding of such mutations. Therefore a gene duplication may be a rare but repeated event, but after that event selection on those copies operates differently allowing neo and sub functionalisation to occur by way of mutations which would have severely compromised the organism if it only had one functional copy of the gene.So while all of the mutations involved, i.e. the gene duplication and the domain or sequences changes affcting function, may all occur sporadically inependently the changes in domain or sequence are able to persist only subsequent to the gene duplication.It is completely distinct from a low frequency allele because for great stretches of time it isn't there at all. you seem to be sliding down to some sort of hidden variable form of intelligent design, like Randman and Syamsu seem to hold bolstered by the wackiness of QM, which is philosophically tenable but scientifically has no value at all. The whole point is that specific mutations aren't predictable!!! That is why it is called random mutation!!! ( Oh dear, excessive exclamation marks!!!!!!!!!) So to support TOE we need to show that random mutations in a population are deterministically predictable? I think we have just gone through the looking glass and are operating on Carrolline logic. I think rather that since you wish to show that the mutations are something other than random then that is what your side of the argument needs to show. You yourself seem to have accepted this now, otherwise why are you reframing the argument in terms of 'truly' novel mutations? Since mutations occur randomly some of them in some environment are inevitably going to produce a benefit to their organisms reproduction. And some of them have as we have seen. Well as I have pointed out given the fact that DNA sequencing has only been viable for a little over half a century and that human generation intervals are estimates as between 25 and 30 years at most we could have information on around four generations at best. Consequently humans are a poor species to study for this sort of thing.The sort of levels of proof you seem to require are totally unrealistic and no actual science will convince you since all the proofs you desire seem to require either a time machine or full time genomic screening of huge human populations. Perhpas with the rise of cheaper genomic screening the second of these will one day be a reality and we will capture many more de novo mutations, although it would take many generations for reliable estimations of fitness. I wonder what rabbit hole you will find to hop down should that day come.Once again it rest on what level of assumption is reasonable given the evidence we have. Percy's conclusion that all the positively selected genes are the result of de novo mutations at some point in the history of life is not generally directl demonstrable scientifically but it is a perfectly reasonable assumption consistent with everything we know about biology and genetics. But if you don't understand the claims in the first place your attempts at unravelling just look like sheer ignorant bloody mindedness because you are inevitably addressing straw men based on your own misunderstandings. That is why people are consistently reccommending you to familiarise yourself with the basic science, because at the moment you don't really seem to have even a basic idea of how the processes of mutation and evolution are thought to work. There are some really excellent biology textbooks available in full online at the pubmed bookshelf.You obviously aren't stupid Faith but given that people have been asking you to familiarise yourself with some of the fundamentals of these issues for years you do seem to be trying for wilful ignorance. You don't have to think like an evolutionist but if you tried to think like a scientist it might help, even if it is an effort. Alternatively I could try and think like Humpty Dumpty if you like, but I'm not sure it would benefit the level of discussion.TTFN,WK

All that is required for an allele to exist 'in potential' is a gene and the existence of the phenomenon of random mutation.How could the ancestral pair of the dog 'kind' on the ark have had all of the allelic diversity required to produce the many forms seen in modern canids? If it lay in potentia in terms of genetics and chemistry then the only known mechanism for it to have reached the potential of actually existing is mutation. That is why people scoff at explanations for explosive adaptive radiation after the Ark as being hypermutational and hyperevolutionary, because starting from a single breeding pair the modern diversity we see would require levels of beneficial mutation and selection many thousands, possibly even millions, of times greater than those we see in nature to be achieved in as little as 4-5000 years. Either that or your initial pair require supergenomes containing hundreds of times the genes we see today.You can see where once again the reasonableness of our assumptions becomes a key factor in evaluating competing explanations. If you don't believe in mutation then you still need another source for the allelic variation we see amongst modern canids or even domesticated dogs.TTFN,WKP.S. Are you still interested in discussing mutation, if so perhaps we should start another thread. Was this thread started here during your ban from the science forums? If that is over then maybe we could move it to a more appropriate venue like the Intelligent Design forum.Edited by Wounded King, : To add P.S.

Mainly that it is clearly completely the wrong forum for the topic. I'm not 100 percent sure that using your admin powers to scoot a topic over into a forum where you don't need to stick o scientific evidence is entirely kosher, but that seems to be being discussed somewhere else.If you are really planning to use the new thread as an opportunity to learn about what actually consitutes mutation then I'm not sure why a science forum like 'Biological evolution' wouldn't be perfectly suitable, what would you need to bring in biblical presuppositions (or perhaps we should say assumptions) for in this case?Perhaps you should start a seperate thread in this forum for discussing your own ideas about mutation and evolution. That would also help to keep the sciencey thread a bit cleaner and might avoid the serious dog piling you seem to be subjected to.TTFN,WK