I was talking primarily about constitutive heterochromatin, including centromeres and telomeres, not transposons. There are islands of genes in this sequence, but much of it is highly repetitive. A lot is functional in bulk – centromeres and telomeres are both vital – but the details of the sequence don’t matter in the same way that they do for what’s normally classified as functional elements.
ETA: As for things like ERVs, there’s no question that some of them are functional, but they’re likely to be a small fraction of the total.
There are no doubt functions which we don’t know about, but there are also positive reasons for thinking that most of the human genome has no effect on phenotype. One is the absence of any sign of purifying selection acting of much of the DNA. Another is the argument from genetic load: if the entire genome were functional, almost all mutations would be deleterious; given the mutation rate in humans, roughly speaking that means we’d all be dead.
The mutation rate probably just scales with the size of the genome, so you’re not really gaining anything by having lots of extra DNA – you just get extra mutations. I’m still perfectly happy to call it junk DNA, by the way. I wouldn’t claim to know for sure whether any particular bit of the genome has no function, but I think it very likely that most of it is junk.
That’s not to say the junk hasn’t had an important role in evolution. Transposable elements, which make up much of the genome and which are the largest source of nonfunctional DNA, are also an important source of new regulatory elements for existing genes, and occasionally of new genes as well. There are intriguing hints that some important evolutionary innovations have relied on the rewiring of developmental pathways by transposable elements. That’s kind of outside my area of expertise, though.
[quote=“glipsnort, post:19, topic:35717, full:true”]
The mutation rate probably just scales with the size of the genome, so you’re not really gaining anything by having lots of extra DNA – you just get extra mutations.[/quote]
Makes sense.
Ultimately I suppose it doesn’t matter what we call it so long as the language isn’t a deterrent to investigation.
In this post I give a one-paragraph summary of some of Dr. Schaffner’s research on the similarity of primate genomes. Long story short: there is even stronger evidence for common primate descent than overall similarity across the genome.
Is your paper an “Origin of Life” paper? Or an Evidence of Evolution paper? While any discussion of these concepts overlap considerably, it’s still easy to see that one topic is much harder to write about than the other.
I recommend the following points be included in a paper on Evidence of Evolution:
the convergence of different scientific disciplines corroborating the extreme age of the Earth;
the pattern of fossil evidence fits no known Creationist scenario:
a. no large mamaal fossils (vegetarian or meat eating) are found with dinosaur fossils (veg. or meat eating); the same can be said comparing terrestrial vs. marine (no ocean dinosaurs found with whales);
b. the pattern of marsupial monopoly and nice divergence (compared to placental mammals everywhere else on Earth) fits no known Creationst scenario;
Speciation is inevitable once two populations are no longer reproductively compatible. The question is how much time does it take, once the populations no longer inter-breed.
the existence of Ring Species and Virtual Ring Species is the closest thing to seeing “Evolution Happening Now”.
Sure. Fortunately, semantic issues haven’t been a deterrent. The function of noncoding DNA has been an active area of research for many decades and is a major focus of research efforts right now.
I’ve always thought the claim that humans and chimps share ~98% of their DNA to be very misleading. I mean, how can a miserly couple of DNA percentage points explain the huge differences between these two creatures?
Maybe you could sign-language that question to the group of chimpanzees that have been taught sign-language. Maybe the answer, the very fact that they can answer at all, can tell you the answer to how different we two primate groups differ.
“…a man shares all but a fraction of his genes with the chimpanzee. But this does not show how alike are man and chimp, but how little genes matter in things that matter.” (from Up Jim River by Michael Flynn)
It’s not a claim, and you’ve misrepresented the fact, as discussed above. They differ a lot more in their non-coding sequences, most of which are junk.
You might like to read a report by Bitten on this topic. 5% difference in the DNA of humans and chimpanzee/great apes etc doesn’t seem much but that 5% actually means that150,000 DNA base pairs are different.
As with many generalizations, your statement isn’t completely true. There are highly conserved regions shared between the chimp and human genomes that share much more than 98%. I think it would be safe to say that, on average, we share less than 98% in regions of junk DNA. In regions of functional non-coding DNA the average is probably higher than 98%, such as with microRNAs which are highly conserved.
Just so we are clear, here are a few quotes from the chimp genome paper (2005)
“Through comparison with the human genome, we have generated a largely complete catalogue of the genetic differences that have accumulated since the human and chimpanzee species diverged from our common ancestor, constituting approximately thirty-five million single-nucleotide changes, five million insertion/deletion events, and various chromosomal rearrangements.”
“Single-nucleotide substitutions occur at a mean rate of 1.23% between copies of the human and chimpanzee genome, with 1.06% or less corresponding to fixed divergence between the species.”
“On the basis of this analysis, we estimate that the human and chimpanzee genomes each contain 40–45 Mb of species-specific euchromatic sequence, and the indel differences between the genomes thus total ~90 Mb.”
So there are 35 million base substitutions which produces a 1.23% difference. There are also 5 million insertion/deletion events that average 18 bases each for another 3% difference. Substitutions and indels are slightly different animals which is why they are listed separately.
I think that in terms of the stated sets, my statement is completely true.
I was trying to make the point that non-coding is not the same set as junk. Junk is a subset of non-coding, so of course functional non-coding DNA is going to be more conserved than non-functional, non-coding (junk) DNA.
If I’ve got my zeros wrong and it works out there are more different Base pairs, that would make the case for difference even stronger. Thanks for your reply.