This is from an email from a friend who is a Ph.D. practicing microbiologist:
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The problem that is rarely recognized is that not all (any?) so-called beneficial mutations fit the needed predictions of evolutionary change by "common descent with modification." Such evolutionary change requires mutations that increase enzyme specificity, create regulatory proteins, transport systems, etc. Examples of these types of mutations are what evolutionists have totally failed to produce. So, for example, an enzyme's ability to degrade nylon is simply the result of a reduction of specificity for that enzyme, enabling it to use a substrate it previously could not use. This could be considered beneficial if there is an advantage for the organism to degrade nylon. But, this, in no way, provides a genetic explanation of how that enzyme's original specificity was formed. Yet evolution claims to account for exactly that, a mechanism of how enzyme specificity originated, not how it became less. Evolution must start at bottom of Dawkins' Mount Improbable, not at the top.
I would also be interested in specific examples of where increased specificity of a protein resulted in antibiotic resistance. There are many examples where the protein loses most or all of the binding affinity for an antibiotic, but this is not the same as gaining specificity within the same active site. I'm not saying there may not be one or two true examples of resistance resulting from increased specificity at the active site, but I have not seen them. And, even so, one or two out of hundreds hardly constitutes a suitable (let alone viable) mutation mechanism for evolution (1 step forward and 500 steps back).
Also, duplicated genes are only providing the organism more of what it already has, thus they offer no explanation of how the organism got that gene originally. And, if one of the duplicated genes mutates so that it has an altered substrate range, we're back to the discussion above, this altered substrate range is the result of loss of binding, specificity, gene expression, regulatory control, etc. So, again this provides no genetic mechanism for common descent with modification (which requires a mechanism that explains the origin of these).
Nor does introducing plasmids or transposons really provide the solution that evolutionists claim. Genetic material on these vectors already exists in the biological world. Introducing them into a specific organism may introduce new genetics to that organism, but not to the biological world as a whole. Hence, transfer of these vectors offers no mechanism for evolution to explain the origin of transport proteins, regulatory systems, etc.
As for sickle cell anemia, genetically speaking this is very much a loss of function (specifically hemoglobin function). Arguments on this in the discussion ...again illustrate a lack of common definition of "function." Sickle cell anemia is the result of a missense mutation of the Beta-globin gene. This mutation causes a reduction of the hemoglobin protein's binding affinity for oxygen. The result is that in the presence of low levels of oxygen, insufficient oxygen will be bound by the hemoglobin, and instead the hemoglobin will tend to malform (ie., sickle). This results in the proteins polymerizing and forming insoluble fibers. These fibers can led to a distortion of the red blood cell shape. But genetically, the mutation must be categorized as resulting in a reduction of protein affinity for oxygen. Therefore, regardless of any claims of a benefit from malaria, etc. the actual genetic nature of the mutation hardly provides a genetic mechanism that accounts for the claims of evolution, ie., a mechanism that explains how life arose through common descent with modification.
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This wipes out any claims for bacteria actually increasing in information regarding nylon digestion! I wipes out claims for sickle cell mutations.
What else are you folks going to offer except faith that "it happened"? What I am seeing from evolutionist apologists here and just about every place I look can be reduced to "My mind is made up. Don't confuse me with the facts."