And yes. Mutations by themselves are never good or bad per se. It is what nature dictates for survival, that says if it is a good or bad mutation.
Using HIV again as the example (since it's quoted already), there are some people around who are naturally more resistant to the virus than others, due to some genes which they possess. In effect, this can be considered a good mutation, handed down from generations, and showing itself only when HIV surfaced in the human population.
H5N1 (bird flu) is the other example. There are some people, as well as birds, and other animal reservoirs, which have evolved/possessed immunity to this deadly disease. This is again due to genetic mutation--or more precisely, genetic variation. Sometimes it's rapid, sometimes it's not. All depends on the species, and the rate of the disease spreading.
note: because of the DNA/RNA thing---genetic mutation tends to occur much, much more slowly in animals, including humans, than in bacteria and viruses. In that sense, the microbes have one-up on us. Plus, one generation in humans is about 25 years, whilst for bacteria/viruses, it may be as short as a few hours. So generational mutation occurs much more swiftly in a same time frame for bugs than for us.
Much agreed!
Stickle cell anemia can be deadly... so why do some many African Americans carry the gene? Because it's a beneficial mutation... For the heterogeneous carrier, 1 normal allele (copy of the gene) & 1 mutant allele, they are less susceptible of catching malaria. It's only when you have 2 copies of the mutant allele that you get the disease.
Mutation is just mutation... random changes. If you have a working system... there are more chances that random changes will impair the system rather than improve it. Perhaps that is why people associate mutation as being a bad thing. It really isn't... it's just RANDOM! Randomly good or bad.
Convergent evolution and evolution in general is always an interesting thing to see... The eye wiring is neat.
Another example would be the opposable "thumb" on the giant panda. They have 6 "fingers"... The ancestorial bears have evolved forward facing digits for running on the ground. The panda developed an appendage to help grip bamboo. Instead of relocating the first digit, the thumb is actually modified bone from their wrist. That's the power of random mutations for you.
There's always more than one way of solving a problem... convergent evolution nicely demonstrates that.
What is a "gene?" I have never quite gotten it's definition from it's usage. Is it a protien? Is it a small sequence of half a DNA-molecule that is known to be responsible for a certain function in an organism? What is it really? In specific/concrete terms?
A gene is a sequence of DNA. With the exception of viruses (they're technically not living) and bacteria, gene sequences are stored together in chromosomes, which are long long strands of DNA all coiled up together. Chromosomes are found within the nucleus (center) of every cell. As it's been said before, it's not a protein. It's the sequence of the DNA that allows for creating specific proteins. And it is the expression of these proteins that forms the phenotype of the individual (phenotype = what the individual looks like, eg hair color, eye color, height etc).
Technically one gene codes for one protein. This is known as the one gene/one enzyme hypothesis. Although multiple genes can produce multiple proteins that can influence a single attribute. Take hair color for example. Textbooks usually tell you that blond hair is recessive (needing 2 copies of blond) and dark color hair is dominant (1 copy of dark is sufficient). But what about the multitude of shades of blond or brunette... what about red heads? Hair color is controlled by multiple genes... However there's a main one that gives you the overall color. The interaction with the rest of them gives you the exact shade.
What does it mean for a gene to be "expressed?" Is it that the through RNA (or whatever comparable mechanism there is in the organism), the identified "gene" creates the phenotype (or rather the little section of it) from the genotype (or rather the little section of it)?
Gene is "expressed" into proteins (mostly enzymes). The exact process is like this:
DNA sequence (gene)-> translated (copied) to messanger RNA -> messanger RNA is processed and sent out of the nucleus -> mRNA is transcribed into (directs synthesis) proteins
Proteins are what makes up cells or acts as enzymes to influence parts of the cell.
Genotype = what gene alleles (copies) you have in your DNA
Phenotype = what is actually expressed... you can see it visibly
Are there quantitative measures of "selection pressure"? IOW, are there somethings analogous to a "
fitness functions" used by computer scientists in synthetic (computerized)
genetic algorithms? If so how does one determine such functions?
I skimmed the wiki articles...
Genetic algorithm appears to be a computer model of evolution... taking factors like selection, chromosome crossover rate, mutation rate etc. The fitness function just tries to describe the selection forces. What might be beneficial for survival.
These parameters are difficult to pin point.
Take the rate of mutation... The rate is affected by the rate of cell division. Every time a cell divides into two, its genomic DNA needs to be replicated (copied). Mistake in the copying gives raise to mutations. So a fast dividing (in the case of bacteria) or fast reproducing (sexual reproduction) organism will have a higher rate of mutation than a slower dividing/reproducing one. Also the error rate of replication is not constant. A cell under stress will mutate faster (hence the use of UV radiation for mutation studies... or UV causing skin cancer). Different species also have different enzymes to copy DNA. Some enzymes have less "proof-reading" abilities than others. RNA retro viruses have an enzyme to copy RNA into DNA for insertion into the host. That enzyme is notoriously error prone and probably have been evolutionary selected to be that way. Afterall, the more mutations it makes... the more difficult it is for humans to come up with vaccines and drugs to stop them.
Selection forces... it's something to keep in mind. Evolution happens far too slowly to be looked at much in real life (with the exception on bacteria, viruses, yeast). So evolutionary studies are based mostly on fossil records and on genomic and protein data we can extract from species that are still alive today. You can't say definitively what the environment thousands of years ago look like. Therefore there's no way to determine what factors are important for survival... Even for current times, you can only guess.
So they can't tell what exactly the selection forces are... but they can tell whether there are sudden changes in selection forces. Sudden change will be indicated in the fossil (DNA) record. With more changes in the DNA genome in the descendant species. (Age can be determined by carbon dating). It's also important to note that much of our genome (90 odd %) consists of non-coding DNA (what's known as junk DNA). Some sections might be necessary... but the sequence of these are not. The amount of random mutation arising in these segments can also be used to track time.
Uhhhh please excuse my rambliness.
mousie. 
