Evolution Requires Reduction in Genetic Diversity

The rates of mutation should be equal across the genome. What differs is whether those mutations accumulate in a given section of DNA. If a section of DNA has function, then there has to be a chance of a deleterious mutation happening in that stretch of DNA. These mutations will be selected against. When we compare genomes, these regions will show up as having more bases in common than in junk DNA where there is no function so no possibility of deleterious mutations.

What you would need to explain is why psuedogenes share sequence homology with functional genes in other species. What evidence do you have that would refute that interpretation?

If that function were important, then the loss of that gene would reduce the fitness of that individual. Those with the mutation that knocked out the gene would be outcompeted by individuals with the functional allele. This would eliminate the pseudogene from the population.It would seem to me that pseudogenes occur when there is a lack of negative selection against mutations in a gene, meaning that the function isn't needed in that gene. How does your interpretation match up better with the evidence than the evolutionary interpretation?

Every time a child dies of hemophilia without passing on that defective gene, it is evidenced. Every time a person dies in their early 20's from Duchenne muscular dystrophy without passing on the gene, it is evidenced. There are tons of examples.

If the space were important then we would see selection against indel events that would be detectable.At the same time, that is a rather rudimentary function akin to vestigial organs or the actual junk in your kitchen. The descriptor "junk" gives us additional information, that the stretch of DNA in question shows no signs of positive or negative selection. This is not true of all non-coding DNA. Also, you no more sequence non-coding DNA than you sequence junk DNA. You sequence DNA. Period. Only afterwards can you determine if a specific stretch of DNA is coding, non-coding, regulatory, junk, etc. DNA takes a tremendous amount of resources? Since when? I don't know for sure, but I wouldn't be surprised if the ATP turnover in one muscle cell from one contraction was equal to all of the ATP turnover needed to replicate the genome of that cell. The problem for the bladderwort was the availability of phosphates to make the ATP, not the energy needed to replicate the genome. Junk DNA and regulatory DNA are both non-coding DNA, and they are very different from each other. As the bladderwort genome shows, 90% of our genome may be disposible, just like the trash in your kitchen.

Then why don't we see evidence of selection against indels in those sections of DNA? How much energy? What portion of a the body's energy is spent on very low level transcription of junk DNA? What harm would be caused by RNA transcriptase that was too stringent and failed to transcribe important genes?IOW, there is a balance between energy and and a somewhat sloppy RNA transcriptase that can more reliably transcribe important genes. If you make RNA transcriptase so selective that it no longer transcribes junk DNA it may not reliably bind to promoters upstream of the genes that you really do want transcribed. Not really the same thing. There are still harmful mutations that can happen in cytC.Being transcribed is not the same as having function.

The tests for negative and positive selection do exist, as do results from those tests. In those results. non-coding DNA is split into categories, one of which is junk DNA.I agree that those tests are not 100% accurate, but this doesn't change the fact that junk DNA is a subcategory of non-coding DNA, and therefore adds more specificity for what you are talking about. They detected negative selection in the several classes of noncoding DNA that they looked at in the D. simulans genome. They aren't making claims about all noncoding DNA in all species. They didn't even make the claim that all noncoding DNA in D. simulans showed signs of negative selection.

If the spaces between genes are important then mutations that change those spaces should be harmful part of the time and be selected against. We do see evidence of negative selection against indels, but only in 10% of the genome. If that were the case throughout the genome, shouldn't we see selection against indels in 100% of the genome? Both of those are empty assertions. In this context, low level transcription refers to the number of copies of any given RNA transcript. For the junk DNA that ENCODE found mRNA copies for, the number of copies were several orders of magnitude lower than commonly transcribed genes such as B-actin. In fact, these areas had so few copies that they had to use special techniques to detect them.If you want to make the argument that the observed rate of junk DNA transcription is energetically expensive then you need to have a handle on the number of RNA copies and bases per copy since the energy is spent making the nucleotides and linking them with phosphates. What matters is the amount of energy that is expended transcribing junk DNA. If it is just 1% of the energy compared to transcribing functional genes then it isn't a problem. When comparing orhtologous cytC genes between species these would show up as regions of conservation. When those are found within an open reading frame, it indicates function. Junk DNA has none of these features. It doesn't have regions that are highly conserved between species. It doesn't have open reading frames that have upstream ribosome binding sites, for example.