Posted by Ayscthian:
"The truth is, you guys really fail. You can't debate properly."
There is, without question, a tendency by both atheist and supporters of evolutionary theory (for whatever reason) to almost immediately label any who question evolutionary theory in any form as first a creationist and then as some form of idiot or imbecile. In fact, the terms are considered to be mutually inclusive. As a veteran of many debates with evolution as its central subject matter, I can attest to how quickly the nature of the responses from the strict pro evolution side turn personal in nature, and the pattern they generally follow. Denigration of any who question or criticize evolutionary theory, especially if worded in a manner which even hints at the notion of either creationism or intelligent design, is the norm.
However, lets see if your comment is correct.
Note also that due to the length of this post, I had to seperate it to comply with site restrictions.
Sometime ago I participated in a thread which discussed, among other topics, the Endogenous Retrovirus, or ERVs. The discussion later turned to include such topics as junk-DNA, RNA, and the RNA World Hypothesis (although the last will not be discussed here).
I have recently found some interesting information I just thought I would share and comment on. Beyond my comments above, I have no hidden agenda. This is just a discussion of a few things I find interesting, and an endeavor to determine what form of response it receives. Additionally, since this is not meant for publication for personal gain, I did not cite references for every definition of every biological term in use. You can find this stuff in any good Biology text.
For background, a Virus is protein shell containing genetic information, or DNA, which can leave a cell. A Transposon, referenced in at least one of the links, is mobile DNA which has to stay within a cell. Viruses function by attaching themselves to a host cell, moving inside, and then taking over the host genetic replication machinery. It transcribes viral genes which code for proteins necessary to produce more virus particles. The viral genome is either DNA or RNA, and those which use DNA do so in the same manner as the host cell. As stated, the DNA is transcribed into RNA which is then made into necessary proteins.
A Retrovirus is one which uses reverse transcriptase to reverse transcribe their RNA genome into a DNA sequence which is then integrated into the host genome.
HIV is a retrovirus.
An Endogenous Retrovirus is one which has been passed through the germ line. In other words, the germ cell contains a copy of the viral DNA, and since all cells in the offspring derive from this single germ cell, every cell in the new progeny would also have the viral DNA.
Junk DNA is the term applied to that some 98% of the human genetic structure which has no apparent function. Junk DNA does not code for proteins, and is therefore said to be genetic garbage, useless, or simply junk. Within a gene, a DNA region containing such junk is referred to as an Intron.
Junk RNA are non-coding RNA molecules, and therefore not transcribed into proteins.
In the evolutionary debate, the question of junk DNA and RNA is no small one. Proponents of ID point to recent scientific findings which indicate that junk DNA is not really junk at all, but does serve a purpose within the cell and in regulation of biological processes. Proponents of strict neo-Darwinian evolution insist that no such thing is true. I have been following this for awhile, and recently put the following pieces together.
I found this over at Science-Blogs, on a sub-forum known as ERV.
Quote:
I was just listening to the 'debate' between Shermer/Prothero and Meyer/Sternberg.
Prothero brought up ERVs, and how they are leftover garbage cluttering up your genome.
Sternberg was all like, "NUH UH! IZ SO HAS FUNKSHUN!!" Its at about 1 hour, 28 min.
Sternberg tries to say that there are lots of 'ERVs' around during embryological development, therefore, PURPOSE AND JESUS!
*snicker*
**SNICKER**
AAAAAAAAAAAAAHAHAHAHAHAHAHAHAHA!!!
End Quote. Link:
http://scienceblogs.com/erv/?utm_sou...edium=dropdown
This is indicative of the debate going on within the evolutionary and/or micro-biology world, between the believers on each side. It can sometimes get pretty ugly. ERVs and junk DNA are said to be the bane of intelligent design. Since junk DNA is useless and serves no purpose it therefore makes little or no sense within the construct of design. It is also said that the very existence of junk DNA refutes the notion of an intelligent designer. Why would a designer create a genome 98% of which served no purpose? The same is said of Junk RNA.
ERVs found to be in the genetic sequence of both chimp and man are said to be clear evidence of common ancestry. When chimp and man diverged, man apparently took his ERVs with him. ERVs make up about 8% of the genome, and were also said to be non-functional or serve no purpose. But yet, some ERVs do apparently have function.
An endogenous retroviral long terminal repeat is the dominant promoter for human β1,3-galactosyltransferase 5 in the colon
Quote:
LTRs of endogenous retroviruses are known to affect expression of several human genes, typically as a relatively minor alternative promoter. Here, we report that an endogenous retrovirus LTR acts as one of at least two alternative promoters for the human
β1,3-galactosyltransferase 5 gene, involved in type 1 Lewis antigen synthesis, and show that the LTR promoter is most active in the gastrointestinal tract and mammary gland. Indeed, the LTR is the dominant promoter in the colon, indicating that this ancient retroviral element has a major impact on gene expression.
End Quote. Link:
http://www.pnas.org/content/100/22/12841.full
LTR is the abbreviation for long terminal repeat, as stated in the title. But this long term repeat, or retroviral element, has a major impact on gene expression. ERVs and retroviral elements are not quite the same things, true. Oh her website "ERV", also know as Abby Someone, states it in this manner:
Well, a handful of endogenous retroviral proteins (not endogenous retroviruses) have been domesticated by the host genome. But this 'explosion' of 'ERVs' is in no way necessary.
But she is in the midst of another of her heated rants against creationist, so whereas I respect her knowledge, I have always held her motives for presenting it suspect. The PNAS article does state that ERVs are known to affect expression of human genes, but is this evidence of the conclusion ERV flippantly refers to as Function and Jesus? Well
.
On the Science Blog website ERV herself goes on to link to a Professor Larry Moran, who also discusses this debate and the issues brought up. He states on his website the following where junk RNA is concerned, material in parentheses added by me.
Quote:
Guttman et al. wanted to identify the small subset that might be functional. They identified 1,675 transcripts that show evidence of conservation (exact generational copies). The average transcript has six exons (an exon is simply a nucleic acid sequence represented in an RNA molecule) averaging 250 base pairs. Thus, each transcript has about 1500 base pairs of conserved exon sequence.
Even if every single one of these lincRNAs (long non-coding RNAs) have a biological function they will only account for 1675 × 1500 = 2.5 million base pairs. This represents less than 0.1% of the genome.
End Quote. Link:
http://sandwalk.blogspot.com/2009/03...-junk-rna.html
0.1% of the genome admittedly is not much. But the ID crowd doesnt take this lying down. Casey Luskin over at evolution news dot org, citing a Nature article, claims that in opposition to being transcriptional noise, over 95% of the non-coding RNAs studied in the paper show "clear evolutionary conservation."
Quote:
That's another way of saying that their sequences are more similar than would be expected if they were functionless and their encoding DNA was accumulating neutral mutations at a constant rate. After all, if such RNA has no function, you can mutate their encoding DNA with no negative consequences to the organism. But if they have function, then mutations in their encoding DNA would tend to be highly deleterious. By finding that they have highly similar sequences, we find evidence of stabilizing selection, which is strong evidence of function.
End Quote. Link:
http://www.evolutionnews.org/2009/03...nkrna_goi.html
The Nature article can be found here:
http://www.nature.com/nature/journal...ature07672.pdf
If it does not come up in full because of pay per view issues, this is from the abstract and is interesting in relation to the study:
Together, these results define a unique collection of functional lincRNAs that are highly conserved and implicated in diverse biological processes.
And this from the conclusion:
"we speculate that many lincRNAs may be involved in transcriptional controlperhaps by guiding chromatin remodelling proteins to target lociand that some transcription factors and lincRNAs may act together, with the transcription factor activating a transcriptional program and the lincRNA repressing a previous transcriptional program."
End Quote.
Functional lincRNAs? If junk DNA and RNA has function, then it can conceivably be evidence for design. Note that Larry Moran was referring to the Nature article as well in the quote I took from his website.
End Part One.
