Distinguishing Design from Accidental Events: Part Three

This is the third and last post related to an Uncommon Descent blog entry debunking some Talk Origins concepts. The UD blog contains powerful arguments against the outdated TO concepts which the reader can access at the link. I'll reproduce the Talk Origins claims and add to UD's referenced data. The UD post items are italicized.

The Talk Origins view of SINEs/Alu:

…current evidence suggests that only a very few Alu sequences are active sources of transcripts; perhaps transcription from most copies is inhibited by the chromosomal environment of the insertion

Further, the excellent health of individuals who lack particular Alu insertions supports the view that these insertions do not serve any important function in human physiology.

As UD indicates, contrary to TO claims, there are many identified SINES known to be functional. Alu sequences, unique to primates, also have been linked to functions.

Furthermore, there is a growing body of evidence that Alu (a SINE) sequences are involved in gene regulation, such as in enhancing and silencing gene activity, or can act as a receptor-binding site — this is surely a precedent for the functionality of other types of pseudogenes. Future studies on the one million Alu copies scattered in the human genome should reveal further regulatory functions of these elements.1

Assumptions underlying the Talk Origins view of endogenous retroviruses are illustrated in the following:

Endogenous retroviruses are molecular remnants of a past parasitic viral infection. Occasionally, copies of a retrovirus genome are found in its host’s genome, and these retroviral gene copies are called endogenous retroviral sequences. Essentially all of these endogenous retroviruses contain mutations that would disrupt the function of their genes, as would be expected if they inserted millions of years ago with no selective pressure to maintain the function of the genes.

The next reference is further evidence cautioning against the assumption of dysfunction.

"More than one million copies of the 300-bp Alu element are interspersed throughout the human genome, with up to 75% of all known genes having Alu insertions within their introns and/or UTRs. Transcribed Alu sequences can alter splicing patterns by generating new exons, but other impacts of intragenic Alu elements on their host RNA are largely unexplored. Recently, repeat elements present in the introns or 3'-UTRs of 15 human brain RNAs have been shown to be targets for multiple adenosine to inosine (A-to-I) editing. Using a statistical approach, we find that editing of transcripts with embedded Alu sequences is a global phenomenon in the human transcriptome, observed in 2674 (2%) of all publicly available full-length human cDNAs (n = 128,406), from >250 libraries and >30 tissue sources. In the vast majority of edited RNAs, A-to-I substitutions are clustered within transcribed sense or antisense Alu sequences. Edited bases are primarily associated with retained introns, extended UTRs, or with transcripts that have no corresponding known gene. Therefore, Alu-associated RNA editing may be a mechanism for marking nonstandard transcripts, not destined for translation."2

More Of UD's reference to Talk Origins claims:

Talk Origins has this to say of LINES:
LINEs thus have several properties expected of “selfish” DNA sequences that can spread in the host DNA simply because they encode their own machinery for spreading.

In other words, they don’t serve a purpose other than to copy themselves, according to Talk Origins.

UD proceeds to document quite a few functions attributed to LINES. UD touches on an area of special interest to me in the mention that LINE-1s are able to integrate themselves into DNA lesions "resulting in retrotransposon-mediated DNA repair in mammalian cells."

Discussed also was a topic of central interest to endogenous retroviruses namely, whether or not they are evidence for common descent. The argument associated with this is based on the belief that their insertions are random and that markers found within corresponding genes of different species would be the result of shared errors.

This linked study shows the need for caution in assuming that SINE insertions indicate common ancestry. From the cited paper:

"Vertebrate retrotransposons have been used extensively for phylogenetic analyses and studies of molecular evolution. Information can be obtained from specific inserts either by comparing sequence differences that have accumulated over time in orthologous copies of that insert or by determining the presence or absence of that specific element at a particular site. The presence of specific copies has been deemed to be an essentially homoplasy-free phylogenetic character because the probability of multiple independent insertions into any one site has been believed to be nil. Mys elements are a type of LTR-containing retrotransposon present in Sigmodontine rodents. In this study we have shown that one particular insert, mys-9, is an extremely old insert present in multiple species of the genus Peromyscus. We have found that different copies of this insert show a surprising range of sizes, due primarily to a continuing series of SINE (short interspersed element) insertions into this locus. We have identified two hot spots for SINE insertion within mys-9 and at each hot spot have found that two independent SINE insertions have occurred at identical sites. These results have major repercussions for phylogenetic analyses based on SINE insertions, indicating the need for caution when one concludes that the existence of a SINE at a specific locus in multiple individuals is indicative of common ancestry. Although independent insertions at the same locus may be rare, SINE insertions are not homoplasy-free phylogenetic markers."3

One more item needs to be addressed which is relevant to inferences drawn from endogenous retroviruses. The origin of viruses themselves have a bearing on theories about endogenous retroviruses. Much of the data ciited in the UD post as well as this one support the theory that viruses have a sub-cellular origin. That is they would have have had some sort of cellular function and would have become independent of cells at some point except for their host dependency. This dependency, as well as the accumulating evidence for endogenous retrovirus function, would support the belief related to their sub-cellular origin.

1. 'Pseudogenes: Are They Non-Functional?'; by Pierre Jerlström; First published in Creation Ex Nihilo Technical Journal 14(3):15, 2000; http://www.trueorigin.org/pseudogenes01.asp

2. 'Widespread RNA Editing of Embedded Alu Elements in the Human Transcriptome';
Dennis D.Y. Kim1, Thomas T.Y. Kim, Thomas Walsh, Yoshifumi Kobayashi1, Tara C. Matise, Steven Buyske, and Abram Gabriel1; Genome Research 14:1719-1725, 2004;
http://www.genome.org/cgi/content/full/14/9/1719

3. 'An Ancient Retrovirus-like Element Contains Hot Spots for SINE Insertion'; Michael A. Cantrella, Brian J. Filanoski1, Angela R. Ingermann, Katherine Olssona, Nicole DiLuglioa, Zach Listera, and Holly A. Wichmana; Genetics, Vol. 158, 769-777, June 2001; http://www.genetics.org/cgi/content/full/158/2/769