Do only advantageous mutations fuel evolution?

I think there is a valuable distinction to be drawn between evolution in terms of the pattern of genetic change in a population and adaptive evolution in which the prevalence of certain phenotypic traits in a population change due to environmental/selective pressures.I think this is the distinction Mayr draws that RAZD referred to.It is also worth noting that as well as providing a foundational basis for further beneficial variation a mutation which is neutral, or even deleterious, in one environment may be beneficial in another.TTFN,WK

I think that Shalamabobi is mis-stating the case by oversimplifying it. There are reasons why neutral and even deleterious mutations can survive in a population, such as genetic drift. Similarly beneficial mutations can be lost by drift. But it is true that what we consider beneficial mutations are those that tend to increase in frequency in a population due to selection, potentially up to the point of fixation.The only way to actually measure the beneficial effect of a mutation is from post-hoc measurements as Parasomnium pointed out.Most mutations are considered neutral, or nearly neutral, but I would suggest it is not possible to definitively show that there is no possible environment in which a particular mutation might have some beneficial, or deleterious, effect. It is however possible to identify many mutations which have little or no likelihood of having an effect, such as in-frame nucleotide substitutions in a protein coding gene which do not affect the amino acid sequence they code for. Even as I write this I am thinking of scenarios where such a mutation could indeed be non-neutral, but I still think there are lots of cases where we can be confident that the mutation will be neutral in most forseeable environments.TTFN,WK

Expression is not the be all and end all of genomic function. There are probably multiple non-expressed sites in what has been considered putative junk DNA which have a functional role, one already identified group of such regions are the 'conserved noncoding elements' (CNEs)(Woolfe and Elgar, 2008). Although as yet the functional roles of all these regions are not clear some have been shown to mediate regulation of nearby genes (Sabherwal et al., 2007).TTFN,WK Edited by Wounded King, : No reason given.

Its the regulation of expression but the sequences themselves are never expressed.You might argue that as functional elements these aren't junk DNA but unfortunately the term is so plastic that there is no easy way to draw a distinct line between what is and what isn't. We suspect that most CNEs have function (or else why are they conserved?) but is conservation enough to mean that a region should no longer be considered junk?Personally, I don't like the term 'junk DNA'. Its especially unfortunate that so many creationists/IDists seem to have decided that somehow some 'junk DNA' being functional is proof of (divine) design.TTFN,WK

I can't really ignore this, it totally redefines the whole concept of gene expression. A gene is 'expressed' when it is transcribed as mRNA from its DNA template, and in canonical cases then translated into protein. To use 'expressed' in some other way is only going to confuse any familiar with molecular biology. You seem to be conflating gene expression and function. Being copied is a distinct mechanism from being conserved. There are some 'junk' elements that lend themselves to increased copying, especially highly repetitive sequences where slippage can occur leading to duplications, but CNEs are usually identified from datasets where such repetitive elements have already been screened out. There still needs to be something acting to maintain the conserved sequence from simply degrading. These sequences are not like ERVs or other remnant proto-viral sequences which can sometimes proliferate through reinfection.If this were merely a case of nearby sequences hitching a ride with selected genes then why do CNEs form islands of such high conservation, why aren't the other nearby sequences conserved?The fact that we are identifying regulatory functions for CNEs suggests that what is going on is more directly relevant to organismal development/evolution than an artifact of genetic hitchhiking.TTFN,WK