stevevw
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Tell that to those who proclaim it as fact beyond doubt. That use it to refute all other options as dead wrong.Theories are not proven. They are only disproven. They are always provisional and dependent on new observations.
Lets start with this.Such as?
Does evolutionary theory need a rethink?

Does evolutionary theory need a rethink? - Nature
Researchers are divided over what processes should be considered fundamental.

No not GMC. Though in principle its a similar idea in that just like humans can modify genetics and environments to produce certain beneficial outcomes over others organisms can have a similar ability developmentally through developmental bias which produces certain phenotypes changes over others.First, what is a "non-random" mutation? Based on the meaning of words that would mean a mutation deliberately induced with purpose. I assume this would refer to, say, GMO crops?
Also developmental plasticity where developmental systems are able to adapt with environments in non random ways due to the connectivity and reciprical relationships between other creatures and environments.
Developmental bias and plasticity assume central roles as generators of novel and coordinated phenotypic variation by conferring directionality on the selective processes. Instead of chance variation in DNA composition, evolving developmental interactions account for the specificities of phenotypic construction. This interpretation is also based on a fundamentally different account of the role of genes in development and evolution.
In the EES, genes are not causally privileged as programs or blueprints that control and dictate phenotypic outcomes, but are rather parts of the systemic dynamics of interactions that mobilize self-organizing processes in the evolution of development and entire life cycles. This represents a shift from a programmed to a constructive role of developmental processes in evolution.
The construction of phenotypic complexity, in which causation not only flows from the lower levels of biological organization, such as DNA, ‘upwards’ to cells, tissues and organisms, but also from the higher level ‘downwards’, such as through environmental- or tissue-induced gene regulation.
The generation of heritable phenotypic variation (variation will be systematically biased and facilitated by the generative features of development
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5566817/
Some work on developmental bias suggests that phenotypic variation can be channelled and directed towards functional types by the processes of development [27,28]. The rationale is that development relies on highly robust ‘core processes’, from microtubule formation and signal transduction pathways to organogenesis, which at the same time exhibit ‘exploratory behaviour’ [28], allowing them to stabilize and select certain states over others. Exploratory behaviour followed by somatic selection enables core processes to be responsive to changes in genetic and environmental input, while their robustness and conservation maintain their ability to generate functional (i.e. well integrated) outcomes in the face of perturbations.
This phenomenon, known as facilitated variation [28,34], provides a mechanistic explanation for how small, genetic changes can sometimes elicit substantial, non-random, well-integrated and apparently adaptive innovations in the phenotype.
Developmental plasticity- Developmental, or phenotypic, plasticity is the capacity of an organism to change its phenotype in response to the environment.
Phenotypic accommodation refers to the mutual and often functional adjustment of parts of an organism during development that typically does not involve genetic mutation [27]. From this viewpoint, developmental processes play a critical role in determining which genetic variants will produce selectable phenotypic differences, and which will not. Genetic accommodation may provide a mechanism for rapid adaptation to novel environments, as those environments simultaneously induce and select for alternative phenotypes [47,52,53].
http://rspb.royalsocietypublishing.org/content/282/1813/20151019
Actually its not and this supports my point that despite claims that the Standard theory has moved on from the gene centric views and of Natural Selection being responsible for all Adaptive variations is still promoted as the main and only forces in evolution.Otherwise we're just talking about selection here. Everything you listed here is just a facet of mutation and selection.
In fact NS is only one of several forces and not particularly dominant and most variation comes from well integrated and non random developmental capacities such as developmental bias, Plasticity, Niche Construction and Inheritence beyond genes such as epigenetics and socialisation.
For example Niche Contruction is also a selective force that can over ride and direct NS, It can work similar to the idea of artificial selection with crops and dog breeds in selecting for the most beneficial and adaptive traits or conditions which are conducive of survival.
In this way it is the organism, the creature that is directing their own evolution rather than being passive entities acted upon by mutations and NS which quite often don't define what is best in the specific situations. Whereas the living creature themselves knows best, understands their environment and are designed with developmental abilities and knowledge to construct their own survivability.
Even culture and other nesting behaviours influence future conditions and therefore what traits will be passed on. According to Epigenetics the stresses a creature lives under will influence phenotype change in how genes are expressed positively or negatively so this points to agency in the choices made to living conditions.
HGT have been found common among all life and this is another means in how genetic info is shared and aids in adaptations especially in simbiotic relationships. So as you can see there is a whole lot more to evolution than just random mutations and NS.
The Standard Eveolutionary Theory (SET) contends biological diversity is mostly explained by natural selection, defined as the confluence of random phenotypic variation, genetic inheritance, and differential reproductive success. However, some scientists (proponents of the “extended evolutionary synthesis,” or EES) are challenging the tenet that phenotypic variation is entirely random and that natural selection is entirely driven by genetic inheritance.
"http://biologos.org/blog/the-changing-face-of-evolutionary-theory"]
Inclusive inheritance- Biological inheritance is typically defined as the transmission of genes from parents to offspring. However, it is increasingly recognized that there are multiple mechanisms that contribute to heredity [59–61]. Parent–offspring similarity occurs not only because of transmission of DNA, but because parents transfer a variety of developmental resources that enable reconstruction of developmental niches [60,62–65]. These include components of the egg and post-fertilization resources (e.g. hormones), behavioural interactions between parents and offspring (e.g. maternal care), parental modification of other components of the biotic and abiotic environment (e.g. host choice) and inheritance of symbionts directly through the mother's germ cells or by infection. In addition, recent research reveals that vertical and horizontal social transmission is widespread in both vertebrates and invertebrates, and can both initiate population divergence and trigger speciation [66].
Under this broader notion of heredity, inheritance can occur from germ cell to germ cell, from soma to germ cell, from soma to soma, and from soma to soma via the external environment [63], The pathways of inheritance that derive from a parental phenotype (‘parental effects’) have a number of evolutionary consequences similar to those of plasticity, cultural inheritance and niche construction [67]. For example, non-genetic inheritance can bias the expression and retention of environmentally induced phenotypes, thereby influencing the rate and direction of evolution [68]. There is also increasing evidence for more stable transgenerational epigenetic inheritance, or the transmission across generations of cellular states without modification of the DNA sequence, which demonstrates that adaptive evolution may proceed by selection on epigenetic variants as well as variation in DNA sequence [60,69,70].
The EES is thus characterized by the central role of the organism in the evolutionary process, and by the view that the direction of evolution does not depend on selection alone, and need not start with mutation. The most striking and contentious difference from the original MS concerns the relative significance of natural selection versus generative variation in evolution, one of the oldest controversies in evolutionary biology (e.g. [116,117]). In the EES, developmental processes, operating through developmental bias, inclusive inheritance and niche construction, share responsibility for the direction and rate of evolution, the origin of character variation and organism–environment complementarity.
http://rspb.royalsocietypublishing.org/content/282/1813/20151019
Probably the overall biggest change would be from the programmed view of the standard theory where creatures are programmed by gene blueprints and acted upon passively by NS. Which narrows things down to genes and NS.What is the biggest challenge? Nothing listed previously seems to be a challenge. Just details of the theory that may further be refined. The overall theory is still very much intact.
As opposed to the more pluralistic view that sees the creature itself at centre as an agent and able to make intelligent and knowledgable choices about its own evolution. That is designed with the ability to adapt both developmentally and intelligently with changing conditions.
We have proposed Evo-lutionary Teleonomy—the idea that organisms can actively affect their evolution on every level—as the new foundational principle of evolutionary biology. Evolutionary Teleonomy unifies many of the independent topics of the Extended Evolutionary Synthesis under a single, understandable label. As has been demonstrated, these principles have real effects on the way that biological facts are used and applied in biological research, and using the wrong principles will lead to incorrect results.
https://www.researchgate.net/public...ciple_for_the_Extended_Evolutionary_Synthesis
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