To try and really quickly answer some of these:
A chromosome is a single long DNA molecule and associated bound proteins - the blobs you see as a chromosome during cell division is way more than half protein. When a cell is not dividing they are decondensed blobs but they fold up neatly into those cords you see in micrographs for segregation during division. A chromosome needs a centromere (point of attachment for fibers to pull it into daughter cells after replication), origins of replication (areas where weak base pairing is pulled apart once per cell division to allow replication to begin), and telomeres (easy-to-rebuild-after-shortening repeats at the ends of chromosomes) if it is a linear chromosome because the ends of linear DNA molecules are difficult to replicate all the way out ot the end.
In a given species the order of genes (and everything else) will be the same on a given chromosome, as within a cell one chromosome is often repaired using the other copy as a template and when generating gametes for sex the two chromosome copies will exchange fragments. Individuals can have differences in the order of genes without having physical problems provided the cut/paste points don't come in the middle of a functional element, though there might be less efficient reproduction when mating with those with the 'normal' arrangement. Over evolutionary time chromosome fragments do break and get shuffled around, but you see between say mice and humans that our chromosomes consist of chunks of an apparent ancestral set of chromosomes that have been differenty cut and pasted back together in the two lineages. Sometimes individual genes move but this is rare.
Asexual species can have their genomes shuffle arond a lot faster because they dont have to stay roughly compatible with their mating partners.
Almost all the time when you have copy number variation of genes, it is due to there being multiple copies of the gene laying right next to each other in tandem. Only a small subset of genes usually have copy number variation, but it CAN exist in a lot of placeswhere it doesn't TYPICALLY exist. These blocks of tandem gene repeats are usually handed down unchanged, but they do change now and then when gametes are being made for sex. When one chromosome breaks and switches pieces with another, if a breakpoint happens inside one of the repeated genes it could attach itself into any of the multiple repeats with similar sequence, allowing one gamete to gain repeats at the expense of another produced by the same parent cell (2 -> 3 + 1, say). As such repeats are unstable and can expand or contract quickly over evolutionary time. I don't know how much research has been done into genes with multiple copy numbers carrying different versions of the sequence.
I changed the old topic because it was misleading and did not convey the questioning intention of this post. Sorry about that.
The point of this post is to examine the proposition that people underestimate the complexity of living beings from examining them through the complexity of their functional DNA included in the genome alone. I don't have sufficient information to answer the question, but I have just about enough information to ask the question, so if you can do a better job drawnig a conclusion that'd be great. Also if you could point out technical errors that'd be nice too.
Genome
The genome contains the DNA which contains each invidual gene and serves as the currency of inherited qualities of the organism. That is evolutionary theories calculate around the frequency of genes and create formalisms, mathematical laws and so forth to predict and understand the phenomenom of natural selection or natural reproduction.
Nothing wrong with this so far. But when it comes to actually thinking about the genes and the protein sequences, it seems to me that often it is forgotten that the entire cell which contaisn the DNA and the mitochondrial DNA and the intracellular devices are part of this replicatory system.
To draw an unreliable surface analogy you could compare the replicatory process to a cellular automata you could think of the system as a generator which accepts a string of numbers to operate the generator. In this surface analogy the entire system is the final organism, the product of the automata, the invidual genes represent the fed in string of numbers and the other parts of the cell - DNA excluded - function as the generator which accepts the string of numbers. This analogue is poor because the distinction isn't real. But it only serves to illustrate a point. Which is that if you have just the string of genome that is contained in the DNA of a human being - you can not make a human being. Something is missing. The devices inside the cells, the mitochondrial DNA, the initial position - which is a fertilized ovum in a suitable environment like the womb.
The point of the post and the proposition is the following:
The genome (mathematically) contains a smaller amount of data than is actually required for an organism as complex as the phenotype produced with the help of it to develop. To illustrate this with the previous surface analogy of a generator and a feed, the complexity of the generator contributes to the complexity of the final product with the fed string. And this leads to cognitive oversimplifying the complexity of an organis. But that analogue is inaccurate, and this proposition could be too.
So can you tell if this proposition is correct or incorrect?
I don't have sufficient knowledge in biology, evolutionary theory, mathematics and I just pretty much can't tell if this is true or completely false, but I'm intuitively anticipating a systemic underevaluation of the complexity of organisms in relation to the complexity of it's genome on these grounds. Note however I'm not saying that people think organisms as less complicated than they're, but in terms of mathematics when extrapolating from the genetic complexity, they'd underestimate their predictions. So what do you think?