-->''I find it elevating and exhilarating to discover that we live in a universe which permits the evolution of molecular machines as intricate and subtle as we.''
-->-'''CarlSagan'''

The fundamental basis of all genetics is that UsefulNotes/{{DNA}} is transcribed into RNA, which is then translated into proteins.

While that statement is pretty simple, in reality the process is much more complex, with lots of details involved that can be changed to affect the final product. The cell itself has many natural checks and balances that control these details and determine when certain proteins are produced and in which cells. The result of this complex regulatory system is a carefully coordinated process of development that starts at conception and regulates the organism's growth, development, and eventual aging and death. An accidental alteration to the gene at some point along the line can potentially screw things up for a few different reasons:

* The wrong genes are expressed
* The right ones are never expressed at all
* The protein that is made doesn't work

This is the cause of cancer, where a mutation in one of the replication control genes suffers severe malfunction and the cell divides out of control.

However, not all changes to a gene are necessarily harmful. Our genetic code has some redundancy built in, and sometimes a single substitution from one nucleotide to a different one will have no effect on the final product at all. Also, changes made only appear as fast as that altered gene is expressed in the cell. For example, if you change a gene that is expressed only early on in life in an ADULT organism, that gene isn't ever going to be used by the organism, and the change will never come into effect.
* A side note: this is one of the biggest challenges with cloning animals from adult cells, in that we haven't quite figured out how to reliably restart the expression of these genes that control these stages of development.

Making changes to different parts of an organism's genome can have different effects, because genes within DNA themselves serve different purposes, and not all parts of DNA actually code for proteins.

Mutations made within the "exons" of a gene (that is, the segments of DNA that actually code for the structure of the protein gene product itself) may affect the structure, and thus the function of the protein made. Proteins happen to be pretty modular in structure, and by inserting new sequences into regions that code for actual protein structure, scientists have been able to tack on new domains to already existing proteins that perform new tasks.
* One common method of studying protein expression in cells is by inserting a sequence that codes for a green fluorescent protein structure into the gene that codes for the protein that they are interested in tracking. When that gene gets translated into the new protein, scientists can pick up the fluorescence from the new domain that is literally attached to the rest of the original protein.

But what about those sequences that are not coding regions? These spots serve as regulatory elements, which signal the cell to express (or stop expressing) other genes at certain times and places. Mutations here can change when and where the protein is expressed, meaning it is made in cells that are not normally supposed to have it, or during a time in the cell's life cycle when it's not normally supposed to be used.
* As an example, if a gene gets duplicated in an organism's genome (an accidental hiccup that sometimes occurs during replication), the new copy can sometimes develop further mutations that affect when or where it is expressed and can evolve to perform new and different functions than the old one.
* Another way of affecting regulation of gene expression is to change genes that code for proteins that specifically turn ''other'' genes on or off (they bind to the regulatory sequences of DNA mentioned earlier, and either allow or restrict the cell's access to a specific gene), and by changing the function of just one of these genes, you can affect entire processes of gene expression within the cell.

However, while random mutations cause undirected changes to DNA, the recent establishment of Genetic Engineering allows us to take a more ''direct'' approach to tweaking genes. Almost all GM research is, yes, currently devoted to picking up genes from one species and moving it to another, as in taking genes found in fish and putting them in tomatoes. In reality, it's much less horrifying then it sounds because our genetic code, using the 4 nucleotide bases that are arranged to code for certain amino acids, is universal across all organisms. Whether you're a tulip, a monkey, or an E. coli bacterium, we all use the same system. However, it's not as easy as just hitting Ctrl+C Ctrl+V...

A useful analogy is to think of DNA as a recipe for a cake as opposed to a blueprint for a house. There is not necessarily a one-to-one correspondence between fragments of DNA and organs of an animal. This leads to three main conclusions:

# Timing is crucial: Adding bits of DNA to a fully grown adult will have negligible or unpredictable results. It's like adding flour to a cake after it has been baked, which will have a different taste and no effect in the cake's fundamental structure. At some point in an organism's life span, the vast majority of its development and cell division is over and done with (e.g., neuron production occurs primarily in the uterus and is minor in adults, hence why people say "brain cells don't regenerate"), just like how the cake is already finished baking.
# The meaning of a gene depends on how it interacts with other genes: Sticking to the analogy here, if you take the "preheat oven" gene from the cake DNA and insert it into the salad DNA it will be useless because the salad DNA doesn't even have genes like "put the salad in the oven". The salad will be unaffected. If you then decide to add "put the salad in the oven" you will simply burn the salad. You can't just give the salad cake properties by taking instructions from the cake recipe and inserting them into the salad recipe.
** Note that rare exceptions do exist. Extending the analogy, it would be like taking the "par-boiled potatoes" genome and adding "preheat oven" and "put potatoes in oven," which will in fact provide you with something edible.
# The actual expression of genes will be influenced by other factors in the environment. Just as the results of a cake recipe may vary due to things like humidity, temperature, and altitude, there's evidence that the results of a DNA "recipe" will vary due to outside influences. Cloned animals often display striking superficial differences from their genetic progenitors because an environment which favors the expression of different genes can coax different results from the same DNA. Apparently, identical twins only are identical because they share the same DNA ''and'' the same prenatal environment. And even then environmental factors during their lifetime can change how their genes are expressed, giving them distinct differences from the same genome.
** Other factors can also affect expression of proteins besides just the cell reading the genes in the DNA itself. Some organisms, including humans, have "alternative splicing", where one sequence of DNA can be read several different ways and produce different proteins depending on which sections of the transcribed RNA (which the cell's ribosomes read to create proteins) are cut and which ones are kept. How the protein is handled after translation is also important, as proteins that are improperly folded (they don't have the right three-dimensional structure) can't perform their necessary function. So even IF everything else is correct, these external factors within the cell can still prevent a gene from working properly.

Genetics is also still a field that is undergoing extensive continued research and is nowhere close to being explained completely yet (although we certainly have come a long way since Mendel's experiments with peas). New ways of regulating gene expression, clues into how mutations help to drive evolution in organisms, and other breakthroughs are still being made even today. This, combined with the potential benefits of such research, like eradicating diseases, prolonging lifespans, and generally improving life conditions for people, make it a scientific area that has gained a lot of attention and interest in the general population recently.