silenzer said:
What I cannot grasp is that, let's say, these birds would have very similar beaks. Some would eventually get the "a bit longer beak" trait, but what are the odds of that happening? If mutations vary from a single gene in a cell located in the foot and to an extra limb being attached, what are the odds of getting a beneficial trait? Aren't they extremely small?
It might help to think about how DNA works and why mutations have effects.
DNA is a very long molecule stored in the cell nucleus. Sections of DNA (the genes) get copied and moved out of the nucleus to other parts of the cell, where small molecules called "transfer RNAs" which have amino acids attached to them, line up along the copy of the DNA sequence. This is how proteins are assembled from a DNA blueprint. Those proteins then go and do whatever they're supposed to do.
A mature multicellular organism has the same DNA sequence in every cell, but different cells are expressing different parts of that sequence, and that is why some are brain cells, others are muscle cells, others are blood cells, and so on. There's a genetic cause for everything.
A mutation is a change in the DNA. This can be a small change in one gene that affects the shape and other properties of the protein that it codes for, or it can be a big change like the complete deletion of a gene, or the duplication of a gene. Duplication events are good raw material for evolution because one copy of the gene can mutate while the other copy preserves the original function. Let's say you have a gene that produces an important digestive enzyme. If it mutated you might lose the ability to digest certain substances and that would be bad for your survival prospects. But if the gene is duplicated, now evolution has a chance to experiment on one copy while the other one still keeps you alive.
In the human genome (and other species) there is actually a lot of redundancy, a lot of old genes that are no longer used but not yet completely deleted, and so on. The human body and the genes that build it are extremely intricate, but they are not perfectly streamlined in how they work. It's even likely that the genome has evolved to be a little sloppy, precisely so evolution can occur. Some species mutate much more than others. This has advantages and disadvantages, and comparative advantage is what evolution is all about.
Anyway, what actually happens when a mutation makes a bird with a longer beak? First, the mutation has to happen in a "germ cell", like an egg cell, so the offspring will inherit it and manifest it. The direct cause of the mutation might be a toxic molecule that damages the DNA a little, or it might be a rearrangement or duplication of several genes caused by the machinery that normally copies genes for readout or checks for errors. Some genes contain repetitive subsequences ('repeats'), and if they correspond to protein structure, duplication of repeats can literally change the shape of the protein that the gene produces. That will change the way the protein interacts with other proteins, and ultimately it can add up to a big change of form. For example, if the protein controls how much growth hormone gets produced, a change in the protein may mean that it stimulates the production of growth hormone much more, which in turn means that certain tissues will grow bigger. That is the sort of mutation that produces a longer beak. The size and shape of organs is due to the way that their constituent tissues grow, and that growth consists of cell divisions, and cell divisions are controlled by internal and external signals like the growth hormone, which in the end is just another protein produced from a specific gene or two.
So I'm trying to sketch how it is that a change in the DNA turns into a change in the offspring. You can see variation in human beings all the time - height, weight, strength, as well as less visible qualities like personality, intelligence, or the way you respond to diet and environmental conditions. There is a basic human genetic blueprint, more or less, and then all the individual people are variations on that blueprint. The variations we see are mostly produced by sex, and the way that the child's chromosomes are a mix of the parents'. But maybe you can see how a mutation in that genetic system is not so different to sexual recombination - it's another way of playing with the blueprint. If the variation is really bad, then the fetus won't even develop properly and there will be a natural abortion. But if the mutation is mild enough to lead to an organism that can live and function in the world, then the new quality has a chance to prove itself in the world of survival and reproduction.
There are genes which control really basic things like the number of limbs. Mutations there are responsible for the big changes to what is called the body plan, the general organization of the organism. Again, most mutations like that (two heads, one eye, etc) are simply fatal, or at least not life-enhancing. Nonetheless, the basic supposition is that the history of evolution over *millions* of years consists mostly of small variations on a settled blueprint, with most big mutations being lethal or maladaptive, but very occasionally getting an extra limb, losing a limb, or rearranging a limb really does allow an organism to do something new and useful in its environment, and it's those events which add up to the big differences in the tree of life - between a worm, a fish, a rat and so on.
What I just wrote is not exactly scientific quality discussion, but I hope it conveys some more of the details.