Junk DNA is a fact. Your own body is filled with it. 96% of your
genome is junk. It has no genes, it has no regulatory function. It's
not used. We know it's not used because it isn't conserved. Only DNA
which is conserved can be considered not to be junk.
If there's no specific or reliable mechanism for removing useless DNA
(and there appears not to be), then junk is inevitably going to
accumulate, especially in organisms which can accidentally bulk up
their DNA by massive duplication like plants are wont to do.
As this Douglas Theobald points out in the fully referenced paper he
posted here:
http://www.talkorigins.org/faqs/comdesc
"Two ciliates, Paramecium aurelia and Paramecium caudatum, are
virtually indistinguishable from morphological and phenotypic
analysis...However, the first has less than 200,000 kb of DNA in its
genome, whereas the genome of the second has nearly 9,000,000 kb of
DNA, which is evidently at least 45 times the amount it actually
needs...Note also that Paramecium caudatum, a single-celled organism,
has about three times the DNA as a human."
As Dr. Janet Young, a postdoctoral fellow puts it here:
https://www.fhcrc.org/about/pubs/center_news/2002/apr18/sart3.html
"Humans dedicate about 350 functional genes to olfaction, the
perception of odors as distinct as a bouquet of roses or a manure-
fertilized pasture. But mice have triple that - more than 1,000 such
olfactory-receptor genes"
But that doesn't tell the whole story. The article referenced above
goes on to say:
"From this analysis, Trask's lab concluded that the mouse genome
harbors some 1,500 olfactory-receptor genes, although about 300 of
those genes are probably nonfunctional "pseudo-genes," copies of true
genes with mistakes that prevent the receptor from working. "In
contrast, humans have about 900 olfactory-receptor genes, of
which nearly two thirds are nonfunctional."
So whilst the mice have lost use of some 20% of their olfactory genes,
humans have lost a whopping 66% of theirs.
http://www.world-science.net/othernews/051207_dogfrm.htm
"Roughly 5% of the human genome has been well preserved by
evolution over the past 100 million years and therefore must encode
important biological functions, the researchers noted. "They also
discovered that the most highly conserved of these sequences are not
randomly distributed throughout the genome. Instead, they are crowded
around just about 1 percent of the genes."
Now this doesn't mean that *only* 5% of the human genome has been
preserved, but it's telling that in 100 million years (that's pretty
much the entire period of mammalian existence), only 5% has been "well-
preserved".
Even if we assume that the entire 5% is in the so-called "junk DNA"
region of the genome - that is, the 98% of the genome which doesn't
encode functional genes - then this still leaves a massive 93% of the
genome which serves no known function and which is *not* significantly
conserved.
Mike Dunford on junk DNA:
http://tinyurl.com/2ont39
T. Ryan Gregory is an evolutionary biologist specializing in genome
size. he has a challenge for you to RUN AWAY from - aimed at those
who claim there is no junk DNA:
http://tinyurl.com/ynkrh2
1) Specify the basis for assuming that all non-coding DNA must be
functional.
2) Specify how one would go about demonstrating evidence of functions
for non-coding DNA in the absence of a framework based on common
descent.
3) Make specific predictions about what function(s) all non-coding DNA
is likely to be fulfilling, and propose ways to test those
predictions.
4) Propose functions for transposable elements that take into account
their parasitic characteristics (e.g., as disease-causing mutagens)
but do not invoke the notion of co-option.
5) Provide a specific explanation for how the great majority of
transposable elements in the human genome can be functional while
showing clear signs of being inactive.
6) Provide an explanation for why the DNA sequences of non-coding
regions in different species appear to correspond to degree of
relatedness.
7) Propose a testable explanation for why similar species may have
widely different quantities of non-coding DNA in their genomes.
8) If one does accept common descent, propose a testable explanation
for how there can be significant reductions in DNA content in some
lineages.
T. Ryan Gregory's "Onion Test"
http://genomicron.blogspot.com/2007/04/onion-test.html
"The onion, Allium cepa, is a diploid (2n = 16) plant with a haploid
genome size of about 17 pg. Human, Homo sapiens, is a diploid (2n =
46) animal with a haploid genome size of about 3.5 pg. This comparison
is chosen more or less arbitrarily (there are far bigger genomes than
onion, and far smaller ones than human), but it makes the problem of
universal function for non-coding DNA clear2.
Further, if you think perhaps onions are somehow special, consider
that members of the genus Allium range in genome size from 7 pg to
31.5 pg. So why can A. altyncolicum make do with one fifth as much
regulation, structural maintenance, protection against mutagens, or
[insert preferred universal function] as A. ursinum?"
T. Ryan Gregory's List of Junk DNA blogs:
http://tinyurl.com/29mydg
1. C-Value
http://en.wikipedia.org/wiki/C-value_enigma "the cells of some
salamanders may contain 40 times more DNA than
those of humans."
Creationists need to explain this. Why would something as relatively
simple as a salamander require 40 times as much DNA as a human? Why
would the bent-winged bat (Miniopterus schreibersi) require only a
1.69-billion-nucleotide genome when it has to fly and operate sonar,
whereas the the red viscacha rat (Tympanoctomys barrerae) require a
genome that is 8.21 billion nucleotides long - four times bigger than
the bat when it would seem to have far less need of it - especially
when you compare that rat with other rats. Creationists need to
explain why this "chosen rat" has so much more of this "useful" DNA.
Or does it just have so much more junk?
If it's junk DNA - the accidental accumulation of the detritus of
evolution needs no explanation. If it's intelligently designed, then
the onus is upon the creationists to explain why their designer
designed it this way.
T. Ryan Gregory also raises this issue in his "onion test":
http://genomicron.blogspot.com/2007/04/onion-test.html "The onion test
is a simple reality check for anyone who thinks they have come up with
a universal function for non-coding DNA1. Whatever your proposed
function, ask yourself this question: Can I explain why an onion needs
about five times more non-coding DNA for this function than a human?"
2. Not all organisms have junk DNA.
If eukaryotes - organisms which share the same cell structure as we
do, no matter how simple or complex - need the junk DNA they have,
then why don't prokaryotes need it?
3. Not all vertebrates have junk DNA.
The highest variability in genome size exists in fish: the green
puffer fish (Chelonodon fluviatilis) genome contains only 0.34 billion
nucleotides, while the marbled lungfish (Protopterus aethiopicus)
genome is gigantic, with almost 130 billion."
They're both fish. They both live in a similar environment. Sure one
needs to breathe air pretty well, whereas the other doesn't, but does
that require it to have almost 500 times as much DNA? Humans breathe
air and we have only one fortieth or so the DNA of the lung fish.
Why?
It's either a matter of runaway junk DNA, or the creationists need to
come up with a really good theory and the science to back it.
4. The huge discrepancies in junk DNA between two similar species As
this Douglas Theobald points out in the fully referenced paper he
posted here:
http://www.talkorigins.org/faqs/comdesc
"Two ciliates, Paramecium aurelia and Paramecium caudatum, are
virtually indistinguishable from morphological and phenotypic
analysis...However, the first has less than 200,000 kb of DNA in its
genome, whereas the genome of the second has nearly 9,000,000 kb of
DNA, which is evidently at least 45 times the amount it actually
needs...Note also that Paramecium caudatum, a single-celled organism,
has about three times the DNA as a human."
So P. caudatum, which is for all practical purposes just the same as
P. aurelia needs *three times* the regulation?
If that's what creationists want us to accept, then they need to do
the science to prove it. Otherwise all that extra DNA is nothing but
junk.
And so of what is junk DNA actually comprised?
1. ERV's
Theobald (referenced above) points out "...endogenous retroviruses
occupy about 1% of the genome, in total constituting ~30,000 different
retroviruses embedded in each person's genomic DNA"
These are viruses which embedded themselves in our genome at some
point over the last four billion years. They weren't even our DNA.
These provide regulatory functions?
If that's what creationists want us to accept, then they need to do
the science to prove it. Otherwise all those ERVs are nothing but
detritus of evolution which now contributes to the massive pile of
junk DNA in the human evolutionary basement.
2. Pseudogenes
Theobald also points out:
"Most pseudogenes are largely non-functional. There are several
lines of evidence that support this conclusion. First, the presence
or absence of most specific pseudogenes has no measurable effect on
organismal phenotype. Second, there are good mechanistic, genetic
arguments indicating pseudogenes have little, if any, function.
Pseudogenes have complex sequences highly similar or identical to
those required for the proper function of other enzymatic or
structural proteins. These normal genes are actively transcribed and
translated into proteins, whereas pseudogenes are untranslated,
untranscribed, or both. Thus, pseudogenes cannot perform the functions
of the proteins they encode. If pseudogenes do have a function, they
must perform relatively simple functions for which the protein encoded
by them was not designed.
"Third, if a pseudogene has little or no function, then most
mutations in the pseudogene will have only minor functional
consequences, and many mutations will not be weeded out by purifying
selection. Therefore, we expect that truly non-functional pseudogenes
should accumulate mutations at the background rate of mutation.
Pseudogenes with minor functions will accumulate mutations near the
background rate. As expected if pseudogenes have little, if any,
function, most pseudogenes accumulate mutations at the fastest rate
known for any region of DNA in animal genomes. Furthermore, the rate
of mutation inferred for pseudogenes from phylogenetic analysis
matches very closely the measured rates of spontaneous mutations."
Note that critical statement that the pseudogenes accumulate mutations
at the background rate - that is, there is *NOTHING* preserving these
genes. Therefore they are unarguably junk. Some 20% of our genome is
composed of pseudogenes.
3. ALUs
Theobald also points out "All mammals contain many Alu elements,
including humans where they constitute 10% of the human genome (i.e.
60 million bases of repetitive DNA)"
10% of our genome is meaningless repeats which perform no function -
not even regulatory.
4. Unnecessary DNA in the genes themselves
Theobald also points out "Only about a third of the 100 amino acids in
cytochrome c are necessary to specify its function. Most of the amino
acids in cytochrome c are hypervariable (i.e. they can be replaced by
a large number of functionally similar amino acids)"
So in this one particular instance, you could throw away two-thirds of
the specifier and miss none of it.
5. Transposons
Theobald also points out "A full 45% of our genome is composed of
transposons, which serve no known function for the individual (except
to cause a significant fraction of genetic illnesses and cancers)"
6. Introns
Within every functional gene are introns. These are purposefully
snipped out and discarded in the translational stage. Do these serve
a function? Do these regulate anything? At best all you can claim
for these is that they are spacers - which is another word for bad
design or for sloppy evolution.
Any creationist who wishes to establish a claim that there is
intelligence in the genome *must* account for all of this refutations
of such a claim.
In the section on "Molecular Suboptimality" at his web page referenced
above, Douglas Theobald raises some interesting issues:
http://tinyurl.com/2h632u
The first is that "A full 45% of our genome is composed of
transposons, which serve no known function for the individual (except
to cause a significant fraction of genetic illnesses and cancers)"
The second is that "Approximately 20% of the human genome is composed
of pseudogenes, the majority of which serve no function for the
individual."
The third item is this: "The majority of eukaryotic genes coding for
functional proteins are interrupted by noncoding sequences called
introns. Introns must be cut out before the information contained in
the gene can be used to make protein. Introns make up 80% of the
average vertebrate gene"
Finally, "The rest of the DNA in a eukaryotic genome is mostly short
repetitive sequences such as AAAAAA, CACACA, or CGGCGGCGG...It appears
that there is no efficient mechanism for ridding most metazoan
(animal) genomes of extraneous DNA"
So having deliberately designed bad DNA into 65% of the non-coding
portion of the genome, and fouled up 80% of the coding portion, this
intelligent designer then went on to sprinkle meaningless repetitive
bases randomly into the rest!
Would you worship a designer who put endless CACA into *your* genome?
Even ignoring the introns, we have fully two-thirds of the genome
which is unarguably junk.
This brings me back to Chicken Macro's "dictionary" analogy. Suppose
you bought a dictionary and found when you opened it that only 1.5% of
it actually defined words?
Supposing when you looked at the other 98.5% you found that almost
half of it had words with no definitions, rendering that part useless
as a dictionary.
Furthermore, supposing when you examined the words more closely, you
discovered that 80% of those words had extra random letters in them
which would have to be snipped out before you could actually read the
word properly?
What if 20% of the dictionary consisted of broken words - words with
letters missing, words truncated before they finished, or words with
serious misspelling?
Seriously. If you bought a dictionary like that, would you *honestly*
believe it was intelligently created by a being who had your best
interests at heart?
Budikka