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+---Topic: "Junk" DNA started by niiicholas

Posted by: niiicholas on April 30 2003,18:28

The topic of so-called "junk" DNA (or, apparently disposable noncoding DNA, more neutrally) has come up endless times in various online debates.  Often, someone will find a new article indicating a function for some bit of DNA, and declare that the "junk" hypothesis is dead and that those evil materialists were blinded by their evil materialism for ever believing it.

The situation is of course much  more complex, so link/post articles, posts (both sides), etc. in this thread.

Posted by: charlie d on April 30 2003,18:41

Funny you should post this today.  The following is coming out tomorrow in Nature:

An expressed pseudogene regulates the messenger-RNA stability of its homologous coding gene
Nature 423, 91 - 96 (2003)

A pseudogene is a gene copy that does not produce a functional, full-length protein. The human genome is estimated to contain up to 20,000 pseudogenes. Although much effort has been devoted to understanding the function of pseudogenes, their biological roles remain largely unknown. Here we report the role of an expressed pseudogene—regulation of messenger-RNA stability—in a transgene-insertion mouse mutant exhibiting polycystic kidneys and bone deformity. The transgene was integrated into the vicinity of the expressing pseudogene of Makorin1, called Makorin1-p1. This insertion reduced transcription of Makorin1-p1, resulting in destabilization of Makorin1 mRNA in trans by way of a cis-acting RNA decay element within the 5' region of Makorin1 that is homologous between Makorin1 and Makorin1-p1. Either Makorin1 or Makorin1-p1 transgenes could rescue these phenotypes. Our findings demonstrate a specific regulatory role of an expressed pseudogene, and point to the functional significance of non-coding RNAs.

The "no-junkers" are going to have a ball - of course without having read, let alone understood a word of the entire article.
Posted by: niiicholas on April 30 2003,18:43

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

< On Paul Nesselroade's current column >


Originally posted by Nelson Alonso:
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.

< >
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.


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:



Molecular melodies in high and low C
Daniel L. Hartl

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:


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:




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.


Posted by: niiicholas on Aug. 14 2003,15:41

Casey Luskin writes:
Link To ID vs Evolution Predictions
< >

< >


4. Genetic Code
Ev: The genetic code will NOT contain much discarded genetic baggage code or functionless "junk DNA."
ID: The genetic code will contain much discarded genetic baggage code or functionless "junk DNA."
'Fact': Increased knowledge of genetices has created a strong trend towards functionality for "junk-DNA"; examples of DNA of unknown function persist, but function can be expected or explained under a design pardigm.


"Junk" DNA
<;t=35 >

The basic observation supporting the 'junk DNA' inference is not pseudogenes -- these are a small fraction of noncoding DNA.  The basic observation is that closely-related critters can have widely-varying amounts of non-coding DNA with no apparent ill-effects.


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.

Charlie d explains it quite well here:
< >


Ironically, the anti-ID letter the DI complains about led me to read an article by a German biologist, apparently an ID sympathizer. Inexplicably, it was published in the prestigious, by-invitation-only Annual Review in Genetics - perhaps because it contained actual information (along with many unsupported and overextended interpretations, but that's just my opinion), and not just a pointless, self-defeating whine like Behe's letter.

Anyway, that paper happens to cite an interesting piece of data that I was unaware of, and which significantly undermines Behe's entire argument that the attribution of lack of function to non-genic DNA is based only on a negative argument (there are many more lines of evidence, of course, but I thought this was nice, especially given the coincidence about the sources).

The data is as follows. These guys (Muntiacus reevesi):

and this (M. muntjak):

are almost identical, they live in very similar environments in Southern China vs. India/South Asia/Indonesia, and just happened to be classified as differnet species because they do not interbreed. The major difference between them is that one has 46 chromosomes and the other 6/7, and one has 20% less DNA than the other, entirely ascribable to the reduction of various kind of non-genic, repetitive elements (ref < here >.

Go figure: a 20% DNA content difference between practically identical vertebrates (by comparison, remember chimps and humans differ by a few % at most). Gee, I wonder why biologists tend to conclude that most non-genic DNA has no significant function. Must be all that "negative argumentation", indeed.


Until IDists start talking about these kinds of facts they aren't even in the ballpark regarding 'junk DNA'.

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