The End of Evolution By Means of Natural Selection

Looks like everyone is bringing their old hobby horses out for a run around the park.Again as you did 4 years ago in Faith's thread on beneficial mutations, Message 208, you bemoan the use of the term beneficial but singularly fail to suggest any usable alternative.Of course a mutation is a change, but those changes have different effects. You seem to have decided to impoverish scientific discussion by not allowing us to use a simple term to describe a particular mutation conferring a reproductive benefit within a certain environment.And of course evolutionists don't say that all evolution is change without implied direction, otherwise we wouldn't have adaptive evolution, presumably another term you object to since of course the organism is only adapted to its current environment.What is the case is that the directions are only implied by the interaction of the genotype with the environment and are therefore highly diverse and labile. The actual mutations are certainly not directional with respect to fitness, but mutation is only one element in the changing population genetics that reveal the constraints that the environment imposes.And no matter how you moan about teleological language you seem to have nothing to replace it with. Anyone with half a brain can tell the difference between terms with teleological overtones which have been co-opted for a technical purpose and actually believing in a teleological process behind evolution and I'm still opposed to butchering commonuly understood scientific technical terms to cater to those lacking half a brain. Should we also be lobbying particle physicists to stop using the terms strange and charm to describe quarks?We shouldn't be censoring and bowdlerising science to appeal to the uneducated who aren't prepared to become educated. Do you really think that if we started using a different term Faith wont still be just as willfully ignorant another 5 years from now?TTFN,WK

So presumably I shouldn't use terms like DNA, transcription, allele, mutation, protein or gene? I mean most of the general public probably wouldn't understand what those terms actually mean would they?We are still in the 'Biological Evolution' forum right? They didn't suddenly tack '...for dummies' on to the end when I wasn't looking? I didn't realise that we had to target the lowest common intellectual denominator in these discussions, I'll try and limit the syllable length in future posts.Its nice of you to confirm that you really are hoping to dumb down the science in preference to having people make any effort to understand what they are discussing.TTFN,WK

Seriously NWR, if you are claiming that Faith's lack of understanding is due to evil neo-darwinists using the term 'Beneficial mutation' then you left reality at a severe tangent some time in the past.You really don't think the popular understanding of those terms, if any even exists, contributes to misapprehensions about evolution/biology? How often have you seen new headlines declaring that scientists have found the gene for something? How many people have a conception of mutation that isn't more firmly rooted in the x-men and sci-fi than in biology? We've had more than 1 creationist come in and spout nonsense that shows they clearly don't even understand the central dogma of molecular biology, i.e. people talking about the amino acid composition of dna. What can I say, it's my 'value added'.TTFN,WK

Well it hasn't happened over the previous five years, so I shouldn't hold my breath if I were you. Nothing has helped, including dozens of people explaining the overwhelming importance of the environmental context of a mutation for it to be judged beneficial in words of one syllable to her.This isn't really a problem unique to Faith of course, it turns up in debate with many creationists. They consider any change from some platonic ideal of a created gene, or presumably in Faith's case a created set of alleles for each gene, to be of necessity deleterious because of course divinely created alleles are the best alleles they can be.Smooth Operator did this a lot, saying that even mutations which clearly produced a beneficial phenotype were deleterious mutations because they changed the protein products conformation, even if the conformation change had no functional effect other than providing the beneficial phenotype.The worst example to my mind was when he claimed that a bacterial enzyme mutating so that it no longer had a high specificity binding site available for an antibiotic to bind to, and thereby kill the bacterium, was a deleterious mutation because the enzyme had lost the function of binding the antibody with high specificity. Admittedly he couched things in terms of genetic information to add another whole layer of obfuscatory bullshit, but the basic premise was the same.TTFN,WK

You are getting a bit mixed up here. Almost certainly what they have is rather a new allele a variant of one of the genes they inherited from their parents. A whole new gene woul be a very much rarer occurrence. A zygote is an embryo at the one cell stage after the germ cells have fused. I'm not quite sure what you are getting it confused with but possibilites would be allele, chromosome or parental gene copy.There is nothing stopping recessive mutations arising. The important thing is the exact nature of the mutation.TTFN,WK

Right, which is why men are more susceptible to things like haemophilia and colour blindness, because the causative mutation occurs on the X chromosome in a region the male Y chromosome does not have a counterpart to so they only have 1 copy of the gene in question. Yes, a novel recessive mutation could easily not give rise to the phenotype for several generations, which means such mutations are good candidates for being lost due to drift.Your example of the desert island seems pretty much right to me.It is worth bearing in mind that there are many traits which don't fall into the simple dominant/recessive categories.TTFN,WK

Have to say I disagree with you here Percy. Within a normal breeding population you are likely to have a spectrum of genetic reproductive compatibility. Given such a situation I can quite readily see a situation where you could produce two daughter populations with distinct strict subsets of the alleles from the parent population but which are not genetically compatible. The loss of alleles or genotypes from the parent population that allowed gene flow between these sub-populations could effectively ensure their reproductive isolation.Suppose there is a gene Fertile with alleles Fertile^a and Fertile^A in the original population. Homozygotes of either allele can breed with each other and with heterozygotes but neither can produce viable fertile offspring with each other. If this population is split and due to drift the Fertile^a and Fertile^A alleles are fixed in respective populations then we will have established 2 genetically incompatible populations without any further mutations, only through loss of one allele from each population. If we reintroduce the 2 new populations to each other they would not be able to breed.Off the top of my head I don't know of any examples such as this, but I don't see why it couldn't happen, or how we would not have to consider the resulting sub-populations distinct species.Given a wide enough panel of genes with alleles giving rise to hybrid inviability we might even see a situation like the Greenish Warbler ring species arising through such a reductive form of speciation.I think RAZD's distinction was that you can't get a genetically reproductively isolated population if another population still exists which retains all the parent populations allelic diversity. In other words, if either of my two Fertile^a/a and Fertile^A/A sub populations were reintroduced to the parent population which still had Fertile^A/a individuals and those of their own genotype in it then they could introgress.TTFN,WK

Hmm, the problem here is that Faith's initial assumption mean we should treat all alleles/ gene variants as if they were part of the hypothetical parental populations complement, unless we can definitively demonstrate a mutational origin for the allele. In most cases we don't have an original parental population to compare to, only two daughter populations. If we accept Faith's framework all of these differences are only those of allele subsets of the original parental population.There are many examples of genes that have been identified as the bases of hybrid sterility and inviability but showing that the origin of those genes was mutational is not possible in the absence of an original parent population, and even with one would require exhaustive genotyping to be certain that the allele was not present anywhere in the original population.TTFN,WK

I think what Faith is talking about is another form of supergenome. She is suggesting that the initial ancestral organisms, in a flood scenario presumably the breeding pair Noah selected, had very high ploidy compared to modern organisms, and therefore had multiple alleles for each gene. There are some modern animals with high ploidy, particularly the various species of Xenopus which can be up to dodecaploid having 12 sets of chromosomes, but even in this case that would give you a maximum of 24 alleles for every gene.It does rather beggar belief that Faith can at once be so scrupulous as to deny the role of mutation in creating standing variation unless we have expirimentally observed the mutation ourselves, something that is well established and routinely demonstrated, but then put forward totally unsupported mechanisms with not a shred of evidence as if they were a sufficient alternative explanation.TTFN,WK

I didn't notice any sarcasm, I think those are exactly the sort of things Faith is proposing, and she isn't the first. Bear in mind that she doesn't seem to have any objection to something like mutation facilitating her fanciful hypotheses, she only seems to object to the existence of beneficial mutations which increase genetic variation in a population. I think all such ad hoc creationist mechanisms are highly prone to the same problem of kind of explaining something but in themselves being wildly improbable.The idea that a creationist will come here with hypotheses that are reasonable, coherent and show any familiarity with biology is itself wildly improbable, I would have thought you had been doing this long enough to realise that?TTFN,WK

I can't see the point in a summary for this thread. It was deja vu all over again from the last time Faith made exactly the same arguments. Lest anyone think this particular bit of nonsense is unique to Faith I would direct them to a post that just went up on Pharyngula describing a very similar argument from a creationist website, although they didn't seem to have gone to Faith's extent of making up highly polyploid supergenomes to allow the flood story to make biological 'sense'.TTFN,WK

It's worth emphasising that the point you raised is important, though your interpretation is a bit off. The mutations for bacterial resistance are not a response to the antibacterial challenge. The trait very likely did exist to some extent before the antibiotic agent was added, although as Taq suggests almost certainly not in the original ancestral bacteria.This is due to the very large numbers of bacteria that can be produced in short periods of time in small volumes and the imperfect nature of genetic reproduction. The initial steps in such experiments is generally to grow up a large number of cells in non-selective conditions, which provides a large amount of random genetic variation which can then be screened for various phenotypes.In some long term experiments it has been estimated that every possible point mutation from the original bacterial genome should have occurred.There are also some experiments which suggest that more specific mutations can arise as a response to certain stress conditions, but that is more controversial.TTFN,WK

As I pointed out before, technically what Barbara says is frequently true, some bacteria can become pre-adapted to a selective medium when grown in a non-selective medium. However the proportion of the bacterial population that becomes pre-adapted is more consistent with random mutation than any sort of microbial foresight.Frankly it was the stuff after what you quoted, when Barbara started going on about collective intelligence, that I would be more inclined to question.TTFN,WK

Only amongst a religously motivated population. No I wouldn't, it would just mean that there are other mechanisms involved. We already know of many such mechanisms, this would just be one more.It is only a creationist strawman that evolutionary theory consists of nothing but random mutation and natural selection. Modern evolutionary theory encompasses a wide range of different mechanisms which are known to contribute to the heritable diversity in a population.TTFN,WK

Well Taq suggested one such mechanism, stress responses which increase the mutation rate for the organism.Another possible mechanism in some cases, especially the Lac frameshift system (Cairns and Foster, 1991), is that low activity genes on plasmids can be amplified independently of cell proliferation. This can serve both to increase the level of gene activity within an individual bacterium and also to produce multiple potential targets for mutations while leaving the mutation rate at its basal level. For a paper discussing some of these factors and suggesting that in fact amplification is not associated with reverting mutations see Hastings et al.(2004), for a further paper suggesting amplification is not responsible see Stumpf et al(2007).A more convincing example of actually 'directed' adpative mutation is the recent paper by Zhang and Saier (2009), where they show evidence for a protein which specifically blocks transposon insertion to a region upstream of a gene for metabolising glycerol but which is downregulated in the presence of glycerol allowing the insertion of the transposon which then drives expression of the downstream gene.TTFN,WK