6) What is the inter-relationship between adaptations of organisms and their surroundings?
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Answer:
It is called Natural Selection.
So evolution comes up with new Mutations which could appear as changes in Anatomy, Morphology and/or Physiology, or something as simple as difference in size, etc. Essentially the genetic tweaking is done by evolution and mutations occur because of imperfections in the gene copying process which in turn could be due to a host of other external or internal factors.
Natural Selection acts to preserve only species with beneficial mutations and eliminate those with none beneficial mutations. Therefore if a species aquries a new feature that reduces its fitness below the fitness limit required for survival in that environment, natural selection prevents the propagation of this defective gene. Natural selection acts to preserve species who's fitness limit are above the environmental requirements.
When Evolution and Natural Selection work together, it creates the scenario where every species that evolve in an environment are adapted to living there and in fact every species fills an evolutionary niche in the environment’s complex survival web.
The last answer i want to discuss with you:
The first thing that needs to be clarified before diving into your question is that organisms don't adapt, populations do. To further elaborate, when we say that this X population of birds adapted to their dry environment by growing larger beaks in order to be able to break the dry seeds, they did not evolve individually. They evolved as a group over generation with individuals having the larger beaks surviving and reproducing future generation that will make up the population, and that is how the population evolve to have larger beaks.
The specific details regarding the molecular pathway that results in variation is rather specific to the trait itself (in addition, mutations are the main source of genetic diversity, while recombination is also considered a source it doesn't produce novel traits/genes).
Now looking at how environments affects individuals and produce an outcome, you need to understand that this can happen on so many levels, and in different intensities producing differential time frame requirement that will also depend on the efficacy of the trait in increasing survival enough to be selective for .
An interesting and hot field of research in the biological sciences is Epigenetics. It's concerned with the changes that are a result of gene expression modification rather than a change in the genetic code.
There modifications are facilitated by chromatin modifiers which modify the structure of the chromatin affecting the accessibility of DNA to transctiption factors, thus affecting the rate of transcrition and it's initiation. ( DNA acetylation increases accessibility in most cases while DNA methylation condeses the DNA and reduced its accessibility)
Whether epigenetic changes are inherited or not is still an ongoing debate that will take some years to solve, hopefully soon.
The link of the paper:
A Conserved Role for Human Nup98 in Altering Chromatin Structure and Promoting Epigenetic Transcriptional Memory
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