Becuase a lot of the new discoveries/changes have replaced Neo-Darwinism as the main force behind how living things change. If you look on this site most people believe that natural selection is the driving force for evolution giving selection a great deal of creative power. That idea is no longer tenable in the light of new information. Natural selection has not only been deminished in its creative power it is said by some to actually be a hinderance to the evolution of complexity.
I think you've either misunderstood what
@Speedwell said or you've conflated the "Theory of Evolution" with "fixation of (rare) beneficial mutations by natural selection" when in fact, the latter is actually just a small part of the former.
There is no consistent tendency of evolution towards increased genomic complexity, and when complexity increases, this appears to be a non-adaptive consequence of evolution under weak purifying selection rather than an adaptation.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2651812/
So, it isn't the case that any aspect of the Theory of Evolution is being done away with, just that the various selection pressures and ways by which that refinement comes about naturally within the Theory of Evolution are now better understood and well documented. For example, if you look at the summary table on this research paper:
Darwinian evolution in the light of genomics - you'll see that the Theory of Evolution still holds true to naturalistic explanations - albeitwith a wider diversity by which it comes about naturally. Why are you going against the very research you posted?
What is in question is whether natural selection is a necessary or sufficient force to explain the emergence of the genomic and cellular features central to the building of complex organisms.
The frailty of adaptive hypotheses for the origins of organismal complexity
Are you even reading these research articles? From the opening paragraph of this one:
"
Although biologists have always been concerned with complex phenotypes, the matter has recently become the subject of heightened speculation, as a broad array of academics, from nearly every branch of science other than evolutionary biology itself, claim to be in possession of novel insights into the evolution of complexity. The claims are often spectacular. For example, Kirschner and Gerhart (1) argue that evolutionary biology has been “woefully inadequate” with respect to understanding the origins of complexity and promise “an original solution to the long-standing puzzle of how small random genetic change can be converted into complex, useful innovations.” However, this book and many others like it (e.g., refs. 2⇓⇓–5) provide few references to work done by evolutionary biologists, making it difficult to understand the perceived areas of inadequacy, and many of the ideas promoted are known to be wrong, making it difficult to appreciate the novelty."
It then goes on to say in the closing comments:
"Closing Comments
Because it deals with observations on historical outcomes, frequently in the face of incomplete information, the field of evolution attracts significantly more speculation than the average area of science. Nevertheless, a substantial body of well tested theory provides the basis for understanding the pathways that are open to evolutionary exploration in various population-genetic contexts. Four of the major buzzwords in biology today are complexity, modularity, evolvability, and robustness, and it is often claimed that ill-defined mechanisms not previously appreciated by evolutionary biologists must be invoked to explain the existence of emergent properties that putatively enhance the long-term success of extant taxa. This stance is not very different from the intelligent-design philosophy of invoking unknown mechanisms to explain biodiversity. Although those who promote the concept of the adaptive evolution of the above features are by no means intelligent-design advocates, the burden of evidence for invoking an all-powerful guiding hand of natural selection should be no less stringent than one would demand of a creationist. If evolutionary science is to move forward, the standards of the field should be set no lower than in any other area of inquiry."
So, the Theory of Evolution remains uncontested, but again, a range of still very natural mechanisms for the success of the theory (rather than just natural selection on its own) are now better understood and well-documented.
Bacteria being able to become anti-bioctic resistant is actually a loss of function ot a gain.
Resistance to the antibiotic can occur by mutations in the 16S rRNA gene, which reduces the affinity of streptomycin for the 16S molecule (Springer et al., 2001). Reduction of specific oligopeptide transport activities also leads to spontaneous resistance of several antibiotics, including streptomycin (Kashiwagi et al., 1998). In these examples, resistance occurred as a result of the loss of a functional component/activity.
Besides anti-bioctic resistance has been around for thousands of years so it designed with the ability
Resistance to antibiotics is ancient
https://www.sciencedaily.com/releases/2011/08/110831155334.htm
I'm not sure if you've missed something here, because even the cited creation "research" you've quoted (not sure of your source, whether it be
Is Bacterial Resistance to Antibiotics an Appropriate Example of Evolutionary Change? - Creation Research Society ,
Islam and Evolution - Ummah.com - Muslim Forum or even
Bacterial resistance to antibiotics: No argument for evoluti ) goes on to contradict itself by giving examples of mutations that change the structure of an enzyme (i.e. not a loss of function after all) to cause a resistance to Ciprofloxacin.
We of course know it doesn't apply to all cases of bacterial antibiotic resistance and the reasons for resistance is varied from case to case. We do know for a fact though that an addition/duplication of genomic material also causes resistance:
Contribution of Gene Amplification to Evolution of Increased Antibiotic Resistance in Salmonella typhimurium
Gene duplication as a mechanism of genomic adaptation to a changing environment <== Not bacterial specifically, but it does touch on the resistance gained by such duplications in bacteria:
"
Many bacteria amplify genes as an adaptive response to antibiotic treatment [36,61,62]. Similarly, it is commonly acknowledged that gene amplifications are known to occur in cancer tumours in response to various drug treatments (see Kondrashov & Kondrashov [36] for review). However, the amplification of genes in response to various drug treatments is not limited to somatic cells and microbes. In the last several years, abundant data have been collected on the amplification of genes in response to various treatments of Leishmania [63] and malaria [23]. The Plasmodium falciparum multidrug resistance gene (pfmdr1) is a target of adaptive evolution in nature in response to the widespread use of chloroquine and other anti-malarial drugs." ..... "It is now understood that pfmdr1 gene duplication occurred independently in nature multiple times [66,69], and malaria with increased resistance to different drugs is found throughout the world from Africa [70] to Asia [71,72] and South America [73]. Finally, at least one amplification event of the pfmdr1 gene shows evidence of having occurred through the action of positive selection [74] and adaptive amplification in P. falciparum has been shown in at least one other gene [75], GTP-cyclohydrolase I (gch1), which is involved in the synthesis of substrates upstream of other enzymes that are commonly targeted by antifolate drugs."
Mutation Rates and Antibiotic Resistance | Learn Science at Scitable <== This one is a Very Good Read! It goes into the many varied ways in which bacteria mutate and grow resistances through massive numbers and random mutations...
Not just that if simple celled organisms are going to change and gain new genetic info it is going to be more likley because of HGT than evolution. Bacteria can also transfer DNA to humans
Bacterial DNA in Human Genomes
https://www.the-scientist.com/?articles.view/articleNo/36108/title/Bacterial-DNA-in-Human-Genomes/
HGT IS Evolution. Why would you think it isn't?
So all in all, it seems you might completely misunderstand what Evolution is. Perhaps if you took the time to understand it better before attempting to refute it? I might make a humble suggestion here...:
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