Friday, January 19, 2007

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 The UD blog contains powerful arguments against the outdated TO concepts which the reader can access at the link.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

13 Comments:

At 7:07 PM, Blogger ERV said...

There is a difference between endogenous retroviruses, Alus, L1s, SINES, etc, and you conflated each of these terms in your review.

Read this and try again:
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=15016989&query_hl=1&itool=pubmed_docsum

Sorry, all of the above are an excellent indicator of common descent.

 
At 7:21 PM, Blogger William Bradford said...

Hello Erv. I don't believe I "conflated" the terms if by that you mean that I gave the impression there was no distinction between them. One of the studies stated the following:

"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."

The paper does not exclude the possibility of a common descent inference. Rather it calls for a cautious approach when the data indicates this to be the prudent course. I've encountered reckless "extremists" representing different points of view who rush to judgement in spite of the particulars that make each instance unique. I'll take a look at your reference though.

 
At 1:02 PM, Blogger ERV said...

Yes, I believe you did conflate terms. For instance, immediately following the quote from TO on nonfunctional endogenous retroviruses, you began discussing Alus. I can whole heartedly assure you that while portions of endogenous retroviruses are functional, you do not want fully functional ERVs. That would guarantee body-wide cancer.
Alus do indeed have a function-- as their sequence similarities added to our chromosomes' ability to rearrange and duplicate, but they are in no way absolutely necessary. I have Alus you dont have. A kid in India has Alus we dont have. The same goes for LINES.

You then go on to conflate ERVs with SINES in the article, and again here in the comments. I realize you arent a retrovirologist, so they all look like bits of DNA hopping around, however they all behave differently. That journal I listed before can help clarify the differences between different kinds of mobile elements. Additionally, I know of no one who only uses SINES for constructing phylogeny (especially in mice), but if there is difficulty at a node, taking a closer look at SINES (among other variables) would be a good idea, due to the behavior of SINES.

And, as far as the last paragraph goes, that viruses were around before cells is not a novel idea invented by ID or writers on UD. Please look up Patrick Forterre. However, I still dont see how any of this is in any way an argument for Intelligent Design, or an argument against evolution.

 
At 6:45 PM, Blogger William Bradford said...

Conflate- to combine (as two readings of a text) into a composite whole. The format followed was the sequence laid out in the linked UD article and my comments were linked to the sequence of comments made in that article. ERVs were frequently cited in discussion groups focused on evolution and intelligent design. The archives of many Yahoo groups are public record. It was not uncommon to encounter the cliche argument that the existence of non-functional elements in a genome was both expected of an evolutionary process and an indication that a designer would have to be stupid to so design life that way.

 
At 5:47 AM, Blogger ERV said...

William Bradford: It was not uncommon to encounter the cliche argument that the existence of non-functional elements in a genome was both expected of an evolutionary process and an indication that a designer would have to be stupid to so design life that way
Thats a false dilemma.
Your god could have put ERVs and various other mobile elements into organisms' genomes to lead humanity to the obvious conclusion of descent with modification. I can see why it wouldnt want to include molecular genetics in the Bible, and why it would trust in our eventual technologies and abilities.
Im just having more and more problems with your, and the UD post, every time I read them. They are positively riddled with errors, but again, I dont blame that on you, because mobile elements are pretty alien to non-virologists or non-geneticists. But yet again, to suggest that mobile elements dont point to common descent with a flashing neon sign is silly, and I dont quite see the point of these articles.

 
At 9:07 AM, Blogger Nathan Munson said...

Yes, I believe you did conflate terms. For instance, immediately following the quote from TO on nonfunctional endogenous retroviruses, you began discussing Alus. I can whole heartedly assure you that while portions of endogenous retroviruses are functional, you do not want fully functional ERVs. That would guarantee body-wide cancer.

No kidding Erv. Nice strawman. It was nowhere suggested that William would want fully functional ERVS.

Alus do indeed have a function-- as their sequence similarities added to our chromosomes' ability to rearrange and duplicate, but they are in no way absolutely necessary. I have Alus you dont have. A kid in India has Alus we dont have. The same goes for LINES.

And your point is what? You can beat up strawmen?

And, as far as the last paragraph goes, that viruses were around before cells is not a novel idea invented by ID or writers on UD.

Neither William nor UD claimed to have invented the concept. Is imputing motives and statements to others that are not factual, a habit of yours?

 
At 9:19 AM, Blogger William Bradford said...

William Bradford: It was not uncommon to encounter the cliche argument that the existence of non-functional elements in a genome was both expected of an evolutionary process and an indication that a designer would have to be stupid to so design life that way

Thats a false dilemma.

No, it's a false argument. It makes no more sense than the argument that a designer would be stupid to design the inevitability of death.

Im just having more and more problems with your, and the UD post, every time I read them. They are positively riddled with errors,

If they were riddled with errors you would have pointed out something more substantial than "conflating." Given that most of my post referenced research papers and UD quotes where are the errors?

 
At 9:34 AM, Blogger Cephus Rocks said...

I can see why it wouldnt want to include molecular genetics in the Bible,

You can see why a historic book, meant to instruct on moral precepts and reveal God, would not want to include molecular genetics? Then again if that subject matter were included, prebiotic pathways to a genome would have been too; don't you think?

As an aficionado of books by Dawkins maybe you can shed some light on this UD quote:

"DNA researcher Andras Pellionisz has found unwitting friends in the ID community. He observed that while Darwinists like Richard Dawkins are dismissive of his field of scientific research..."

Was Dawkins dismissive? If so why?

 
At 7:42 PM, Blogger ERV said...

Nathan Munson: No kidding Erv. Nice strawman. It was nowhere suggested that William would want fully functional ERVS
I believe it was. Immediately following a paragraph from TO saying ERVs are not fully functional, William Bradford said:
"The next reference is further evidence cautioning against the assumption of dysfunction."

Clearly indicating that Mr. Bradford would like someone to discover a fully functional ERV to support his other assertions that all DNA is useful.

Nathan Munson:And your point is what? You can beat up strawmen?
Mr. Bradford seems to think that Alus are functional and necessary, given his citations in this article.
Alus are useful for things like duplicating an arm of a chromosome and alternate splicing and such, so over a long period of time they are in retrospect 'necessary' though at the time they were not.
The fact that you and I have different Alus illustrates that point. If all Alus are necessary, one of us would be dead. In a few million years, maybe your Alu will co-op something fun, and not having your Alu would be deadly.

Nathan Munson:Neither William nor UD claimed to have invented the concept. Is imputing motives and statements to others that are not factual, a habit of yours?
To the casual observer, it absolutely looks like this is an idea invented by ID, and look at the silly Evolutionists that didnt know.
I realize that blog writing is very casual. If Mr. Bradford did not mean it that way, Im sorry. Perhaps me pointing this out will help better your alls writing skills so this sort of confusion is prevented in the future.

 
At 7:57 PM, Blogger ERV said...

Cephus Rocks: You can see why a historic book, meant to instruct on moral precepts and reveal God, would not want to include molecular genetics? Then again if that subject matter were included, prebiotic pathways to a genome would have been too; don't you think?
*laugh!* Could you imagine how thick it would have to be to include all of that?? LOL My biology books would add a good 50 lbs at least, and theyre paperback! Ugh add in all the physics and chem... I would have hated to be the guys making copies of the Bible before the printing press!

Cephus Rocks: As an aficionado of books by Dawkins maybe you can shed some light on this UD quote:

"DNA researcher Andras Pellionisz has found unwitting friends in the ID community. He observed that while Darwinists like Richard Dawkins are dismissive of his field of scientific research..."

Was Dawkins dismissive? If so why?

Im afraid I was not present when these two individuals met, so I have no idea whether Dr. Dawkins was dismissive, much less why he was dismissive or not.
Perhaps it would have been prudent for Dr. Pellionisz to ask Dr. Dawkins himself if he felt slighted? That certainly would have made things easier.

 
At 9:03 PM, Blogger Nathan Munson said...

William Bradford said: "The next reference is further evidence cautioning against the assumption of dysfunction." Clearly indicating that Mr. Bradford would like someone to discover a fully functional ERV to support his other assertions that all DNA is useful.

Cautioning against the assumption of dysfunction does not equate to wanting a discovery to support an assertion that all DNA is useful. Worse yet Mr. Bradford did not claim that all DNA is useful. In making that allegation you are lying. Anyone reading the post can see you are putting words in his mouth.

Nathan Munson:And your point is what? You can beat up strawmen? Mr. Bradford seems to think that Alus are functional and necessary, given his citations in this article.

That's an unwarrented assumption on your part. He does not believe that and the "evidence" you cite reflects your projections.

If all Alus are necessary, one of us would be dead.

There was never a claim to the contrary. As I've indicated you are good at demolishing strawmen.

Perhaps me pointing this out will help better your alls writing skills so this sort of confusion is prevented in the future.

The confusion is a creation of your mind. You need a remedial reading comprehension course or a course on ethical behavoir depending on the source of your problem.

 
At 2:23 AM, Blogger Cephus Rocks said...

Cephus Rocks: You can see why a historic book, meant to instruct on moral precepts and reveal God, would not want to include molecular genetics? Then again if that subject matter were included, prebiotic pathways to a genome would have been too; don't you think?

*laugh!* Could you imagine how thick it would have to be to include all of that?? LOL My biology books would add a good 50 lbs at least, and theyre paperback! Ugh add in all the physics and chem... I would have hated to be the guys making copies of the Bible before the printing press!

A description of documented prebiotic pathways to a functional genome would take up no space at all. If you had confimation of such pathways you would be Nobel eligible.

Cephus Rocks: As an aficionado of books by Dawkins maybe you can shed some light on this UD quote: "DNA researcher Andras Pellionisz has found unwitting friends in the ID community. He observed that while Darwinists like Richard Dawkins are dismissive of his field of scientific research..." Was Dawkins dismissive? If so why?

Im afraid I was not present when these two individuals met, so I have no idea whether Dr. Dawkins was dismissive, much less why he was dismissive or not. Perhaps it would have been prudent for Dr. Pellionisz to ask Dr. Dawkins himself if he felt slighted? That certainly would have made things easier.

The claim was that Dawkins was dismissive of a field of scientific research; not that anyone felt slighted. Regretably you have twisted the words of others since you began posting comments. You don't need to do that.

 
At 3:38 AM, Blogger William Bradford said...

This post is closed to further comments.

 

Post a Comment

Links to this post:

Create a Link

<< Home