T. Ryan Gregory:   I think your comments are on the right track, but the one quoted here is problematic.  It is not the case that this idea is held as the explanation until it is refuted when there is no supporting evidence.  The burden of proof is on proponents to show why this idea should continue to be taken seriously.

Yes – here I mean that more complex theories should not be proposed in preference unless there is good evidence for them – of course that is exactly what I have been doing with protective vs. null, as explained in the other post on your later edition of the junk story!
 

Keith Grimaldi: find a long lived species with no “junk”;

“No junk” is a pretty strict requirement, but here’s an interesting one.  The red sea urchin, Strongylocentrotus franciscanus, has been reported to live up to 100 years.  It has an estimated genome size of only about 800Mb.

Keith Grimaldi: It just seems to be one of the simplest explanations that should be dismissed (with evidence) before proposing more complex hypotheses (without real evidence).

I think your comments are on the right track, but the one quoted here is problematic.  It is not the case that this idea is held as the explanation until it is refuted when there is no supporting evidence.  The burden of proof is on proponents to show why this idea should continue to be taken seriously.

1. No significant lifespan is possible with a sequence dependent functional only genome – I don’t know offhand what “significant” is, but at least  it would predict that in any creature living for more than few years the genome will be mainly “junk”, or not sequence sensitive

2. If the bulk of DNA is “junk” then sequence preservation will not be important and will not be conserved. Take some skin fibroblasts from an individual and make monoclonal cultures from them, sequence and compare coding vs “junk” regions to compare mutation rates in different genome areas between different cells from a single individual. This will be possible in the not too distant future with “next-next” gen sequencing (whole genome in sequenced in 15 mins!). For now maybe it could be speeded up a bit by culturing in a mutagenic medium and sequencing long stretches rather than whole genome.
3. Mitochondrial DNA will not need protection because of the number of copies per cell. Random mutations will not become established, just like a single strain of e.coli will remain the same strain unless selective pressure is applied

4. Removal of large portions of non-sequence conserved “junk” DNA should shorten life span – this i suppose would be technically tricky

5. Refutation – any of the following:
a) find a long lived species with no “junk”;
b) show that majority of DNA is highly sequence sensitive;
c) removing “junk” has no effect on damage induced aging;
d) explain how a “coding only” genome could sustain mitochondrial levels of damage;
e) demonstrate other functions for the majority of the non-coding DNA;

Chris Lawson: “I think that long stretches of non-coding DNA will increase the chances of higher-level replication errors (e.g. Fragile X syndrome, Down syndrome).  ”  OK, but does it really? and does it increase mutation or are the errors detected and cells killed by apoptosis

Who moved the goalposts and where by the way??
 

1) What specific, testable predictions does your hypothesis make?

2) What evidence would you accept as refuting the hypothesis?