The End of Evolution By Means of Natural Selection

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

Aside from drug resistance, I don't understand why this forum does not believe that anything is possible with these single celled organisms. I read many articles from science that explain the many ways in which these organisms adapt and some were noted to prepare for a future change in their environment in advance, that they do appear to use collective intelligence and have many ways to communicate with one another and to other different species of microbes. The enormous data of how they are responsible for maintaining life in our own bodies as well as the entire planet is amazing. They are miniature biochemists and the earth appears to be their laboratory and we are their lab rats. Single celled organisms do not even belong under the term evolution because they are in a class that is way above our human abilities to fully comprehend it let alone try to translate their biochemical language .

Maybe there is an opportunity here to get funding to do a super-genome study now that the RATE study has been terminated..As futile as this thread may seem, that futility is also generated in the mind of the reader, who siding with you is thinking, why can't she(faith) get it, who sees her denying reality(no beneficial mutations when the number of human mutations from parents to offspring has been measured etc), who sees her ignoring the short legs on dogs being an example of a dominant trait that's non-existent in the parent population, etc.I think a YEC that reads through this will likely have some other ad hoc theory in mind and might see the fallacy of faith's and perhaps begin to recognize the pattern of failure of "creation science" thinking - find an apparent fault, not a real fault, just some "what if" hypothetical fault, and use it to bring into question the whole theory, all the while ignoring the available facts that disprove your "what if" scenario.One can only hope.Of all the ToE misinformation out there, probably the idea that mutations are not "beneficial" to adaptivity is the greatest stumbling block of all. Mutation is random and undirected. How can this be beneficial?In mathematical terms it allows the whole domain-space(of possibilities) to be searched, it makes it accessible (for optimization of adaptation).
If all mutations had to be beneficial this would be analogous to optimization by following the steepest gradient (slope).An example is finding the highest terrain in the wilderness. You would head uphill until you reached the top of the mountain you're on. But you might look around from that vantage point and see another mountaintop a ways off that is even higher.This is the shortcoming of the idea that all mutations have to be beneficial. It allows the discovery of local maximums only. If you found yourself partway up a hillside and saw that an adjacent mountain was taller than the one you were on, you would realize that to get to the highest ground, you first had to descend again.This is how improvement occurs from randomness.Of course the rest is filtering the random results for the best adaptations. This occurs in nature from the competition for resources. This is why the ratio of "bad" to "good" mutations is irrelevant.. This filtering occurs in the mind as well when we undertake to learn with the objective to prove a particular outcome. We gather data and sort it into bins. The bin that re-affirms our beliefs we fill with all we can find.The bin that represents refutations to our beliefs we bury in a dark corner. And so we can evolve our thoughts and world view in a direction contrary to what is generally known to be true. If you are harboring incorrect beliefs, as you gather more knowledge at some point it is no longer tenable to maintain those beliefs. They must either be abandoned or modified
to achieve harmony with what you now know to be true.This is growth and it is healthy and good. In order for this false world view(YEC) to remain, competing facts and knowledge must be eliminated.
And that's reduction in acceptance of the real world, or last thursdayism.. Edited by shalamabobbi, : No reason given.Edited by shalamabobbi, : more spelling..long thread burnout..

If you can show me any experiments demonstrate precognition in bacteria I should be most grateful. And surprised, of course.

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

Evolution by means of natural selection is also controversial.Wouldn't you agree that if these experiments turn out to in fact be true, that that essentially shatters the entire notion of evolution by natural selection? Isn't that what makes them controversial?When bacteria is "prepared" to make a mutation in response to certain pressure, we have certainly opened a whole new door that can't be shut.I am not naive enough to believe that most of the believers in Darwinian evolution would ever actually release their frozen grip around their theory, but there would at least be some that have keep their skepticism alive enough to begin to look elsewhere for truth.

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

Quorum sensing in bacteria is well below what is seen in multicellular eukaryotes like ourselves. I wouldn't describe so much as intelligence but as an automaton. Bacteria have set reactions to a set of stimuli, but they don't really show an ability to improvise. Actually, bacteria are often the best type of life to use when testing the theory of evolution. Their generation times and ease of growth make them ideal for studying the theory.

Evolution solely by means of natural selection is controversial. The most famous of these experiments is the emergence of lactose metabolism due to metabolic stress. When the first studies came out they made a rather obvious mistake. They assumed that the mutation rate didn't change. It does. When DNA damage occurs due to metabolic stresss or antibiotic treatment this turns on the SOS response. This response includes the production of error prone polymerases which increase the background mutation rate. It also turns on recombinases which can copy a gene multiple times.So what about the lactose experiments? Well, it turned out that the presence of lactose did not cause the mutations to happen. Rather, the lactose rich environment SELECTED for the lactose mutations and lactase gene duplications. There was no mechanism that sensed the presence of lactose and then produced the needed mutations to metabolise lactose. These mutations occur at the same rate no matter if lactose is present or not. These mutations are random with respect to fitness. Show me the evidence and I will gladly do so.

What is the mechanism that you are proposing is responsible for bacteria generating a mutation in response to a selective pressure?

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

From that very article..."The mechanism for such mutation in stationary phase is not known, but it requires some function of RecA which is apparently not required for mutation during exponential growth."Is there a reason why you said this is one possible mechanism, when the article that you referenced says the mechanism is unknown?And from the paper by Zhang and Saier:"Directed mutation is a proposed process that allows mutations to occur at higher frequencies when they are beneficial. Until now, the existence of such a process has been controversial."And how does this support the notion of Darwinian evolution? What explanation does Darwinian evolution offer for directed mutations?I have all along believed that adaptive mutations occur, but I can't see any which in which this bolsters your evolutionary theory. I can see lots of ways in which it contradicts it however.

The reason is because that reference is the original one for the Lac frameshift experiment, the other papers are the ones discussing subsequent studies of possible mechanisms. A mechanism which is unknown in 1991 may have been discovered since then.TTFN,WK

I may be restating some info here, but:
When (these particular?) bacteria get put in an environment that isn't exactly the most conducive to their survival, they go batshit and hit the panic button - the error-prone polymerases that Taq mentioned. That makes more mutations happen in the same time, effectively speeding up the evolutionary process: more mutations can be acted upon by external factors, and it is more likely that one which enables lactose/lactase (is the latter a typo, or both actually used?) metabolism will arise. Those bacteria that are more likely to produce/produce more of the polymerase are more likely to survive in the adverse environment, because they are more likely to find a beneficial mutation before the population is eradicated by that environment, and thus also more likely to pass on the "panic button" alleles/genes.Quite simply, a trait that increased the number of traits which could be selected for, was selected for. Meaning that it propagated through the population, leading to a better survival rate in times of stress.
Evolution itself, in fact, enabling evolution to occur more quickly. At least, that is how I would explain it from the evolutionary perspective. Maybe real professional biologists think otherwise (but it would be cool if they didn't ).

What you have described here fits the explanations for the Cairns experiment but not the Zhang and Saier paper that Bolder-dash was asking about.TTFN,WK