Does the Darwinian theory require modification or replacement?

If you're gonna hang your hat on "genetic assimilation", I suggest you do your research. Start here.

qs=Shadow71Not sure of the accurracy of this, but I take it to mean that all mutations that are not beneficial are destroyed, or not picked, in some way.[/qs]As you know I am not a biologist. I can only infer from what actually happens, ie. the end result. I cannot describe the molecular process.What appears to be happening here is that beneficial, deleterious, and neutral mutations occur in a specific locus. Then somehow only the beneficial mutations are selected.
How this selection works is what is important, not what you call it.
How can you know the selection is "natural"? and how do you define natural?
Is selection random?, if it is random how did it occur that only the beneficial mutations were selected, and if it is non-random then isn't it directed in some way?

As I mentioned earlier, both neutral and deleterious mutations accumulate at the locus.
Please provide a cite (from the research literature!) that supports your contention that only beneficial mutations are selected.

You seem to have a gross conceptual error regarding selection. Only the beneficial mutations are selected for what? You seem to believe that selection is something that occurs before the mutations are passed on to offspring. Am I reading you correctly?That is not what Shapiro or Wright present in their papers. Shapiro says that selection (i.e. purifying selection, or negative selection) happens due to competition for resources in a new ecology. That's clearly selection after creating/conceiving a new entity with a non-random mutation. I would think the answer to your question, as presented in Shapiro's paper ought to be obvious given the above, and an understanding of what natural selection means.

Not only are you not a biologist but you seem to have little to no grasp of any of the terminology associated with evolution.Natural selection is not an active operating force, it is the name given to the observed patterns of differential success between different genetic variants. What determines those patterns is the environment in which the organism exists. Selection works, in the extreme sort of cases studied here, because organisms which are incapable of surviving in a given environment will have a drastically reduced chance of contributing their genes to subsequent generations. Over time, over multiple separate experiments as well in some of these cases, we can track the patterns of gene prevalence and see which ones are successful in a specific environment. Generally selection is categorised as natural or artificial, artificial selection is what is practised by human livestock breeders and agriculturalists to produce novel strains or to breed for specific characteristics in an animal or plant. So natural selection is selection without a human agency directing it.Humans choose traits for the benefit of humans so the sort of things that result from artificial selection and the strength of it, as seen by the associated genetic patterns, tend to be different from natural selection which essentially shows the effects of all the organisms traits interacting with the environment simultaneously.If you mean how can we know that selection isn't the result of capricious invisible fairies then the answer is that we can't but what we know is that the interaction between the environment and the genome appears sufficient to explain what we observe. So what purpose is served by positing intangible and unnecessary additional entities? No, even asking that question suggests you don't understand even the basics of evolutionary theory. The effect of random changes in the prevalence of particular alleles from one generation to the next is called genetic drift. Genetic drift results from a wide variety of phenomena from localised freak environmental factors up to extreme population crashes causing bottlenecking. It is essentially a result of random sampling of the genetic makeup of the population. This represents a fundamental misunderstanding of selection and beneficial mutations. The only way to determine what mutations are beneficial is as a result of studying their success. So the fact that a mutation has been positively selected is what tells us it is a beneficial mutation. We can estimate to some extent what mutations will be beneficial, but only in very limited controlled circumstances where we have a very good understanding of the organisms genetics and the specific environmental challenges involved. In many experiments there will also be neutral mutations occurring and it may require a considerable number of generations or experiments to be able to definitively discriminate between patterns due to selection and those due to drift.Just to emphasise, no one says that natural selection is random.TTFN,WK

Let me give you a simple example of natural selection.Suppose an individual is born with a mutation that renders it completely sterile.Then (by definition of sterile) that individual will have no children. So the gene will never spread through the gene pool of that species. When that one individual dies, then the gene pool says goodbye to the bad mutation. This is an example of "negative" or "purifying" natural selection.How do I know it's "natural"? Because what could be more natural than that a sterile individual should have no offspring? It would be a miracle if it did.Is it "random"? No, it's a stone-cold certainty.Is it "directed"? Again, no. There's no need for an intelligent process to step in and assess the situation and say to itself: "Hmm, this is a bad gene, I'd better make sure that it doesn't get reproduced." The badness of the gene itself ensures that it won't get reproduced.This is what we call "natural selection".As I say, this is a simple case. It's simple because it involves a gene for complete sterility. Once you've got your head round this, we can go on and look at more complicated cases if you like. But this example gives you the basic idea.

I think you're exaggerating.It is true that it would be hard to say a priori what effect a given change to the genotype would have on fitness, but only because it is presently very hard to figure out what effect it would have on the phenotype. However, it is often very easy to figure out the likely effect on fitness of a mutation considered as a phenotypic variation.So for example we do know a priori that a mutation conferring resistance to an antibiotic will (other things being equal) be advantageous to bacteria exposed to that antibiotic. It is true that we cannot presently parlay that knowledge into being able to say: "And so it would be beneficial for this base just here to change from A to C"; that would be more difficult.

That is what I meant, "a mutation conferring resistance to an antibiotic" is not any specific mutation but rather a wide class of different mutations whose molecular nature we don't know. Also your 'other things being equal' covers a multitude of possible antibiotic resistance conferring mutations that also negatively affect the organisms reproductive success enough to outweigh the benefits.Certainly the frequency of one of that particular class of mutations arising is interesting from a pop. gen. perspective, but knowing the actual molecular bases is much more informative and certainly much more relevant when one is discussing directed mutation.TTFN,WK

There are other scientists who seem to belive she is worth citing in their papers.Here is an example. The paper can be found at:Interciencia – Revista Interciencia

Shadow.
It's simple.
Either cite Ho's published research or find another paper published in the research literature that supports your claim of directed mutation/directed evolution.

If so could you please summarize it in your own words. I, for one. do not fully understand what they are trying to actually say. Please in layman's terms explain the point they are trying to make and how it supports your idea that evolution is directed.ABEDo you think non-random = directed?Edited by Theodoric, : No reason given.

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Facts don't lie or have an agenda. Facts are just facts

I'd like to second that, Theodoric.
The article he linked to doesn't discuss directed evolution or directed mutation.

The only thing I can figure is what I added by edit.He must think that non-random means the same thing as directed. I would like to get a clear answer from him on that and an explanation as to why he thinks they are the exact same thing.

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Facts don't lie or have an agenda. Facts are just facts

I tried to explain to him that nonrandom is not the same as directed a month ago in Message 125. He ignored it.He's just searching paper titles for key words like "nonrandom" and then saying they support his position without getting into understanding what the paper is actually saying.Don't waste your time.

I gave him a definition of directed evolution in Message 390. Source. The definition even cites the Cairns paper he tried to use upthread. I also pointed out that a Cairns collaborater had to walk back that definition in 1999. Source.