Mutation

Hon, I don't know it for exactly 'coz i'm also just a student, but I'm sure that there are some advantages for intermediate stages. Let's say it needs a, b, c, d to form a perfect knee joint. First, there was no knee joint, and then b by mutation, a particular orgnism had an 'a'. There would be some advantages for having 'a' rather than not having any of them. So, that guy got selected for. In this way, the gene that codes for 'a' allele became dominant in population. then 'b' allele might arose from mutation. If 'a' and 'b' allele came from the same species, sex will help the combination of these two alleles and they would outcompete the guys which had only either'a' or 'b' alleles."The eyes of moles and some burrowing rodents are quite covered up by skin and fur. This state of eyes is.....aided perhaps by natural selection". (Darwin)

Yup,agree. As far as I know, mutations in junk DNA are neutral. So do the third codons of the DNA/ RNA, genes that codes for inactive sites of the proteins. Whatever genotypes which can't be seen by natural selection.

What do u mean by "a loss of data"?

To say the truth, I know very few abt Gladyshev thermostat.In my opinion, j_Dna is neutral 'coz it can't be seen (sort of) by natural selection. In the origin of life, DNA evolved as they got the more stable forms to keep info(also say by thermostat law). After billions of years, some selfish genes managed to make their self-copying stuff as junk dna; never got translated or transcribed. i think 'feed back' things don't apply in this case. Besides,these j-dna are evolving at pretty fast rate (by drift )compared to other protein coding dna.
For mitochondria, it is saaid that about 85% of changes in mitochondria is silent. As far as I know, it was once free living bacteria has it own genetic info, but i don't know how important is the proteins that mitochndria genes code for.
sorry about thermodynamic thing. I have no idea about that. Actuallly, I don't get how thermodynamic plays important role in evolution of organsms which are open systems.Got any info that can make me clear abt that? thanks.