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  Topic: "Junk" DNA, Towards a FAQ on "Junk" DNA< Next Oldest | Next Newest >  
niiicholas



Posts: 319
Joined: May 2002

(Permalink) Posted: April 30 2003,18:43   

Here is a post I wrote in response to Nelson Alonso:

Link:
On Paul Nesselroade's current column

========

Quote
Originally posted by Nelson Alonso:
 [QUOTE]
Key scientists agree they are now obliged to abandon the term "junk DNA".

The large stretches of genetic material formerly known as "junk DNA" are now acknowledged to contain important instructions essential for life.

www.gtg.com.au/asx121202.pdf
Which is what lead to Dr. Eric Lander's statement about humans.
[/QUOTE]Please, Nelson, this is some kind of company press release and gives no details about how what the function is.

   
Quote
[QUOTE]
While you're at it you might try explaining the function of the DNA in near-identical sister species, where one species has 50%+ more than the other.
Sorry this is a little vague. Can you give me a reference?[/QB][/QUOTE]Gee, you haven't heard of this kind of thing, yet you have made all kinds of authoritative pronouncements in this thread?  How surprising...

For example:

 
Quote

Molecular melodies in high and low C
Daniel L. Hartl
OPINION

For 50 years now, one of the enigmas of molecular evolution has been the C-value paradox, which refers to the often massive, counterintuitive and seemingly arbitrary differences in genome size observed among eukaryotic organisms. For example, the genome of the fruitfly Drosophila melanogaster is 180 megabases (Mb), whereas that of the European brown grasshopper Podisma pedestris is 18,000 Mb. The difference in genome
size of a factor of 100 is difficult to explain in view of the apparently similar levels of evolutionary, developmental and behavioural complexity of these organisms.


The C-value paradox emerged from among the first applications of spectrophotometric analysis of nuclear DNA content1. The haploid DNA content of eukaryotic organisms ranges over a factor of 80,000. Some of the largest genomes are found among the lowliest of eukaryotes, such as the amoebae, and some of the smallest genomes are found among organisms with complex developmental
and behavioural repertoires, such as Drosophila melanogaster. These discoveries were made before the elucidation of the molecular structure of DNA or its genetic coding function, so it is  understandable that massive differences in DNA content were difficult to interpret. In the subsequent two decades molecular biologists laid out the molecular mechanistic framework of life — replication, transcription, translation and mutation. But at the culmination of this period, the C-value paradox was as great a mystery as ever. Maybe the paradox lay within ourselves.
What if our concepts of organismic complexity were backwards? Perhaps the lower forms actually do have more genes — maybe, in fact, “they require more genes to conduct their dreary affairs”2.

DNA renaturation kinetics carried out on many eukaryotes showed that genomic DNA contains many moderately or highly repetitive sequences, the relative amounts of which can differ markedly from one species to the next3,4. Many of the differences in genome size can be attributed to differences in the abundance of these repetitive sequences, rather than to large differences in the nonrepetitive fraction of unique DNA, which
includes the coding sequences5.

(bolds added)

Folks, *these* are the observations that led, and still lead, to the "junk DNA" suggestion.  Unless a junk DNA critic comes up with an explanation for why species A will have 100 times as much DNA as very similar species B, they haven't explained "junk DNA".  The question is (1) why are eukaryotic genomes primarily made up of repetitive sequences and (2) why can the amounts of these sequences vary so much within closely-related groups?

IDists who talk about junk DNA with out bringing up the above observations front-and-center are not even talking about the actual issue.

More quote:

 
Quote
Large-scale genomic sequencing gives a quantitative picture. On the long arm of human chromosome 22 (REF. 6), only 39 per cent of the DNA sequence resides in annotated genes, including
their introns, and only three per cent resides in the exons of the annotated genes; in contrast, about 42 per cent of the chromosome consists of tandem and interspersed repeats of various kinds, including 16.8 per cent Alu repeats, 9.7 per cent LINE 1 repeats, and 3.8 per cent LINE 2 repeats. On chromosome 21 the situation is similar, but with only 26.2 per cent of the DNA in annotated
genes7. To a large extent the C-value paradox is due to the proliferation or diminution of repetitive elements.

The players
Some of the main mechanisms for change in genome size are shown in FIG. 1. We include chromosomal mechanisms, such as polyploidy and accessory chromosomes, even though these mechanisms are prominent only in certain lineages, particularly in plants.  In some lineages in which polyploidy does take place,most of the differences in genome
size in different species are nevertheless due to other causes. For example, the fact that wheat (genome size 16,000 Mb) is hexaploid accounts for only about 8 per cent of its genome size relative to that of rice (genome size 430 Mb), because the wheat genomes contain large amounts of repetitive DNA that are not present in the rice genome.

Figure 1 | Principal mechanisms for changes in genome size. In a large genome, such as the human
genome, the protein-coding DNA is sparse and interspersed with non-coding DNA; at the scale shown here, coding DNA would be invisible. Except in some plant lineages, polyploidy is not a principal cause of variation in genome size. Insertions and deletions differ in size as well as in rate among species of organisms.
Now, FWIW, I think there is some good evidence for "function" of a sort of "junk DNA" -- namely, the total amount of DNA in a cell correlates well with cell volume.  This would indicate that "junk DNA" serves a "skeletal" or "spacer" function, or alternatively that larger cells have less selection pressure for mutational deletions. This would be a function, but it is not very sexy and not sequence-dependent.  The article quoted above cites some of the literature for those who are interested:

Nature Reviews Genetics article

Here is the bit I'm talking about.  As you can see, there are a variety of "live" hypothesis among evolutionary biologists, both pro- and anti- "junk", even though they are supposedly all nasty materialists:

 
Quote

[...]

FIGURE 1 focuses on the mutational mechanisms that can change genome size, but natural selection may act on the genetic variation created by mutation. With regard to selection for genome size, there is an extensive literature on potential adaptive functions of non-coding DNA, much of it related to correlations between genome size and cellular traits (notably nuclear volume) or organismic traits (notably developmental time)8. Amoebas, with among the largest genomes, also have among the largest cells; in describing an entamoebal infection in 1890,William Osler9 observed:

“They are most extraordinary and striking creatures and take one’s breath away at first to
see these big amoebae — 10–20 times the size of a leucocyte — crawling about in the pus.”

Limitations of space preclude an extensive discussion here, but the varieties of adaptive hypotheses for the maintenance of non-coding DNA include the ‘skeletal DNA’hypothesis10, according to which non-coding DNA functions as part of the basic framework for the assembly of the nucleus and serves to regulate nuclear volume in relation  to cell volume; and the ‘buffering DNA’hypothesis 11, which posits that non-coding DNA buffers condensed chromatin from intracellular solutes, and uncondensed chromatin from nonspecific DNA binding by proteins and their ligands.

Conversely, views of non-coding DNA as merely accumulated ‘junk DNA’12 or self-perpetuating ‘selfish DNA’13,14 stand against these adaptionist models of genome evolution. Recent evidence showing that non-coding DNA is subject to elimination comes from studies of cryptomonads and chlorarachneans15,16. In these organisms, the descendants of ancient symbioses, the nucleus of a former algal partner persists as a simplified ‘nucleomorph’, surrounded by a periplastid membrane; in different lineages, the nucleomorph has undergone a 200–1,000-fold  reduction in genome size with the elimination of virtually all of the non-coding DNA.

  
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