This is a repost from the old ERV. A retrotransposed ERV :P I dont trust them staying up at Blogger, and the SEED overlords are letting me have 4 reposts a week, so Im gonna take advantage of that!
I am going to try to add more comments to these posts for the old readers-- Think of these as 'directors cut' posts ;)
WHOO! Classes over! Scary 'wait for grades' time begins... But Im finally going to get to jump into an ERV series Ive been wanting to do for a while! It will hopefully turn into a great resource for all you science defenders when you encounter a Creationist online/real life, as ERVs are a super cool way to demonstrate common descent and evolution in action!
Here is a (monster) repost of a list of Creationist Claims I hear a lot about ERVs-- if you dont totally understand this post now, stick with me :) Im going to go through all of the basics of ERVs, their components, and what they mean for evolution, and you will totally be able to get this stuff!
Claim 1-- ERVs do not exist
Courtesy of a new source of blogfodder: ERVs do not exist.
Endogenous retroviruses (ERVs) are segments of DNA which, due in part to some similarities and their seemingly haphazard distribution, are thought to have resulted from past viral infections.
Even if this idea were correct, it does little to support evolution in the microbes-to-man sense.
... and so on.
This is part of a larger Creationist scheme-- put words like 'purportedly' and 'supposedly' in front of basic scientific facts. Create confusion in followers by making facts relative. "We look at a sequence and see GOD! Scientists look at a sequence and see MUTATION! Same data, different interpretations... You arent a MUTATION, are you?"
The LTRs of ERVs are distinctive enough that we can sometimes determine what kind of retrovirus the ERV used to be (alpha, beta, etc). We can even find families of related ERVs and reconstruct an infectious retrovirus from their leftover bits. There is no other way to 'interpret' this data, other than stating that ERVs are ERVs.
Claim 1a- Biologists make up 'ERVs'. ERVs do not exist.
Via Uncommon Descent commenter JoeG, who has 'forgotten more about ERVs than youll ever know'*:
Fact 1- A virus can be manufactured just by matching a sequence
Fact 2- That we think we see ERVs in genomes (or fragments of ERVs) means that there is a sequence match.
Take those two facts together and it is easy to see one can create a virus even if there was no virus originally.
See? ERVs are just like the Bible Code for evilutionists! You can make a genome say anything you want! Know a retrovirus sequence? Just by chance, if you match a retrovirus sequence with a human sequence, youll think you see ERVs there! But they arent ERVs-- Theyre... something else (dont ask him what).
In the end, pertaing to ERVs, all you have is that "they look like ERVs to me". If that passes for science then "It looks designed" also passes.
Unfortunately, thats not how bioinformatics works (intro genetics must be part of that ERV stuff that JoeG has already forgotten). If Bible-Code bioinformatics were possible, the entire field would be useless-- you couldnt separate the wheat from the chaff. The fact of the matter is, bioinformatics, especially regarding ERVs, is precise. Different families of retroviruses leave distinct footprints in our genome. It is not magic.
And, retroviruses becoming endogenous entities is not a magical occurrence that only happened long ago in a galaxy far far away-- we can study retroviruses in other organisms that are exogenous and endogenous. We have genetically modified mice that lack specific ERVs so we can use them as controls in ERV activation experiments.
Its not magic.
JoeG touches on several Creationist Claims Ive already discussed, but I wanted to highlight this claim because it is a fun bit of irony. Radical Christians using the Bible Code to predict who the Antichrist will be and when the Apocalypse will happen is just superduper! But misunderstanding bioinformatics and virology to say evilutionists make genomes 'say anything they want' is UNACCEPTABLE! lol.
* Gratuitous Arrogant Creationist Claim
Claim 2-- Retroviral Insertion is not Random. Common Descent is an Illusion.
Ive always said, if Darwin and Wallace decided to open a resort and spa in Cuba instead of going into science, if every fossil was still hidden-- The second we found ERVs, common descent would have smacked us in the head like a sack full of doorknobs.
You can play connect-the-dots with ERVs to draw phylogenetic tress, like they did here (okay, a little more complex than connect-the-dots hehe!)
So the logical claim from Creationists is that this apparent common descent isnt real. Retroviruses (and mobile elements) could have inserted themselves in chimpanzees and humans independently, and we cant prove otherwise.
Here are two papers that Ive seen Creationists use in support of this claim.
- Retroviral DNA Integration: ASLV, HIV, and MLV Show Distinct Target Site Preferences
- An Ancient Retrovirus-like Element Contains Hot Spots for SINE Insertion
You can probably figure out from the paper titles why Creationists latched onto these two. 'Site Preferences'? 'Hot Spots'? Insertion isnt random, therefor apparent common descent is an illusion!
Unfortunately if they had, you know, read the papers they referenced, they would know that the papers do not support that conclusion, and do not contradict the usage of mobile elements as phylogenetic markers.
The first paper simply states that some retroviruses like to insert in genes, some like to insert near promoters of genes, and some like to insert in the middle of no where. The specific insertion sites, what base pairs on on the left, which ones are on the right, is random. Thats exactly what they looked for in that papers methods.
Look at Figure 1: All those blue lollipops are places they found where HIV inserted itself.
Theres a lot more than one lollipop in that figure. The Creationist Claim is wrong.
The second paper gives them a quote to pirate, and while the statement is true, its not true in the way Creationists want it to be.
The presence of a retrotransposon at a single locus inmultiple taxa remains an extremely powerful phylogenetic marker,but caution is required before concluding that the existenceof a particular SINE at a particular locus in multiple individualsis indicative of common ancestry.
These researchers found two independent SINE insertions in deer mice. They could tell the insertions apart. So their caution was for geneticists making phylogenetic trees-- look closely at your SINEs to make sure they are really related, and not independent events. Something they should be doing anyway, but its nice to know that you might find independent insertions while you are double checking it.
Their conclusion is that retroelements are just dandy for phylogenetic analysis. Again, this Creationist Claim is wrong.
Claim 3--You cant use ERVs to support common descent. Not every organism has them.
On the one hand, Creationists accept the fact ERVs point to common descent. On the other hand, ERVs pointing towards common descent is unacceptable to Creationists. Thus the Siamese twin of "Common Descent is an Illusion" is born-- "You cant use ERVs to support common descent. Not every organism has them."
The claim I am referring to specifically states that ERVs do not exist outside of mammals. This is not true. ERVs have been found in marsupials, zebra fish, birds, snakes, toads ... Every vertebrate weve looked at has had ERVs.
Evolution only predicts that organisms susceptible to retroviral infection would have ERVs, and those ERVs would form a pattern of descent with modification. Thus far that prediction has held up.
Claim 4-- Creationists Predicted ERV Functionality.
A main Common Creationist Claim about ERVs is that they predicted ERV functionality before Evilutionists. Evilutionists refused to study ERVs because they are 'junk.'
Parts of ERVs are functional. For instance, the env gene of specific endogenous retroviruses has been co-opted by mammals to form placentas (I elaborate here). Also, endogenous viruses carry genes with them called LTRs. This is how an exogenous virus like HIV uses an LTR-- but when the virus becomes endogenous, the LTR can act as a promoter for endogenous genes, either up or downstream. This paper has a humorous, but accurate name for this: "domesticated long terminal repeats".
Evilutionists did this research, not Creationists. Evilutionists predicted functionality in non-coding regions, not Creationists (see MarkHs post at Denialismblog). ERVs and host co-opting and pirating ERV parts is a prediction made by evilution, not Creationism.
Claim 5-- Evolution didnt predict ERVs, so ERVs arent evidence for evolution.
This is probably the most pathetic Creationist Claim about ERVs. No, I did not make it up. Its right there in TrueOrigins 'Critique of +29 Evidences of Macroevolution '.
Evolution does not even predict the existence of ERVs, much less that they will be found at the same location in two or more species. After all, evolutionary theory was considered robust prior to the discovery of ERVs.
Evilution as Darwin knew it did not predict ERVs, specifically. Mostly because DNA, RNA, retroviruses, sequencing, etc etc etc werent discovered yet. Yes, the theory of evolution worked just fine before any of those things were discovered.
Whats important is that their discoveries supported natural selection and descent with modification, thus influenced modern evilutionary theory in a positive fashion (science, unlike dogma, is not static. this is a good thing).
Over and over and over, ERVs can be traced back to create a phylogenetic tree. ERVs and their components descend with modification over time. Sometimes these modifications lead to junk, sometimes they are coopted by their host, sometimes they become such an integral part of the host that it is almost impossible to tell the DNA is exogenous.
ERVs themselves werent predicted by Darwin, but what they do and how they behave was. Descent. Modification.
Claim 6-- ERVs are functional.
As a defense against the argument that 'junk DNA', including nonfunctional ERVs, is evidence against their choice* of 'Designer', Creationists insist that ERVs are functional.
There is a very big difference between a functional ERV, and a functional component of an ERV. Creationists do not understand this (specific example here)
Yes, we have found a retroviral env that has been co-opted by mammals. Yes, somewhere around 100 human proteins might have evolved from co-opted gag proteins. Yes, we can find retroviral transcripts floating about cells, sometimes. But these are not examples of ERV functionality. They examples of evolution in action-- the host organism salvaging ERV parts for its own use.
Complete ERVs are recombined, mutated, and methylated into junk. When they regain some semblance of functionality, they cause disease! Which is no surprise, as exogenous retroviruses like HIV and HTLV cause AIDS, leukaemia, lymphomas, and various other autoimmune diseases.
ERVs specific to humans, called HERVs, have been tied to multiple cancers, including germ-cell tumors, breast cancer, seminomas, melanoma, ovarian cancer... And autoimmune diseases like multiple sclerosis, rheumatoid arthritis, psoriasis, and lupus (please see this source for more information).
These are just the human-specific ERVs. We have lots more.
DISCLAIMER-- Currently, ERV->disease research is very new, as are the methods we use for studying why they become active (epigenetics). 'Functional' ERVs might be the cause of disease, the effect of disease, or both (the effect, but perpetuates the disease, what I think is going on with ERVs and cancer).
But one thing is certain thus far-- You do not want ERVs to be functional.
* This argument is inappropriate when discussing 'design' with polytheists, deists, or those who believe in a malicious deity. I believe it is also incompatible with theistic evolution. This stance only applies to Creationists.
Claim 6a- ERVs are a 'vaccine code'.
ERVs are somehow 'built in vaccines' placed into genomes by the Designer. Ive seen the following paper used as evidence to support this claim:
This claim also suffers from the same misapplication of inductive reasoning as its parent claim (6). A part of an ERV can be a helpful defense against a related exogenous virus means ALL ERVs are 'vaccines'. Yes, parts of endogenous retroviruses that are still active can interfere with infection with related exogenous retroviruses-- Both of those papers involve a virus that has exogenous and endogenous versions (enJSRV vs JSRV). This paper (and related papers) do not hypothsize that every ERV has an antiviral function.
With good reason.
Any ERV proteins that are expressed as your immune system is developing are recognized as 'self'. If a T-cell or a B-cell recognizes this viral protein as 'self', it is killed. Sometimes this can lead to an enhanced infection from exogenous retroviruses, even bacteria, because entire branches of your immune system are killed off!
ERVs are not specially designed 'vaccines.'
Claim 7-- Non-functional/Harmful ERVs are _________.
If you know the appropriate response to 'ERVs are functional' you will undoubtedly see its Siamese Twin Creationist Claim: 'Non-functional/Harmful ERVs are _________.'
The blank can be a variety of things.
- The result of The Fall.
- The result of The Flood.
- They used to be useful, but arent needed anymore.
- They have some hidden use that scientists havent found yet (such as a 'built in vaccine'- which will be covered later).
- They are tricks embedded by their god to test His Creation.
- The ever useful 'we cannot know the Designers thoughts'.
- Conserved non-functional DNA is evidence for a Young Earth, etc.
This Creationist Claim is always in response to the 'ERVs are functional' refutation. Ignoring the philosophical and logical problems with 'answers' like "ERVs are a test!" these claims are ad hoc non-answers-- They do not address the discord between ERVs and Special Creation (common descent, domesticating exogenous genes, etc.), or why this discord does not exist between ERVs and evilution.
If you encounter a ________ youre not sure how to address, please leave a comment
It's probably BS but this creationist says that ancient retroviruses played a role in modifying the p53 "master gene regulator," so ERVs might actually have a benefit after all and therefore fit into God's wonderful creation.
Quick question from someone ignorant of the details of the ickier sciences: could junk DNA/nonfunctional ERVs be considered "useful" in that, treating point mutations as more or less stochastic (maybe this is a bad model), their presence increases the chances of any given mutation being neutral, rather than screwing up something important?
Just something I've been curious about lately
It's been a while, but that might work for some cases. Excess DNA would buffer mutagens, but it would have no effect on mutations caused by replication errors. I'm not sure what the balance is between those types of mutation. It's purely an accidental benefit though (of course, that's true for a lot of things to do with mutations...)
Steve-- One point I really really want to stress to everyone is that ERV functionality/dysfunction isnt an argument for Creationism. What is an argument for evolution is that these ERVs (and other mobile elements like them) follow a pattern of common descent, useful or no.
Its like a connect-the-dots game that points to evolution!
Bosons & Owen-- Well, your genome has had to evolve ways to control mobile elements, which is also useful for controlling our genomes too!
I was almost done with my blogs and now I have thirteen new tabs open. Damn you and PZed for making biology so interesting. Things were so much easier when I was just a chem nerd.
So then ERVs aren't really evidence against creationism because they can serve some strange yet beneficial purpose. But the placement and differences in ERVs across species is uniquely evidence for evolution.
A friend of mine and I were having a discussion concerning that ever-friendly topic of macroevolution. Sigh... I presented him with alot of ERV evidence and links, but I am unable to explain to him why the following is not the case. Could you either explain how we know ERVs are random enough to serve as markers, or to save your breathe, provide me a link that can explain this principle. His quote is below.
"Finally, regarding the similarities: Is it likely that similar species are susceptible to similar retroviruses? I'm sure that there are lots of RVs that attack only primates and nothing else. Therefore, those ERVs would only affect us primates, not pigs. ...Viola! someone finds evidence of ERV on primate DNA and not pig DNA. BIG friggin' shock!!! Yes, I realize that part of the Neo-Darwinist argument is that the random strains of ERV DNA are *exactly* the same in these similar species, a mathematically-unlikely event. However, the mathematical significance of this is only *significant* if you can demonstrate that the specific ERV in question DOES NOT leave ONLY a specific strand of DNA. (WoW! That was a complicated sentence. Let me put it this way --> ) A specific ERV leaves an A-C-A-T-A-A-G-G-T-C-C-A- ... -A-T-T-T-G-G-C-A-T-A strand on all common primates. In order to demonstrate the mathematical significance, you have to demonstrate that the specific ERV COULD leave a strand that wasn't A-C-A-T-A-A-G-G-T-C-C-A- ... -A-T-T-T-G-G-C-A-T-A. I contend that it is *possible* that the ERV only has a very specific strain of RNA that it wants to pass on. Therefore, that strand would be present in all species affected. If, at some time in the past, there was an outbreak in a certain area, then all primates in that area would be affected. Those strains get passed down until today, when scientists interpret the evidence as evidence of common descent. That is a REASONABLE conclusion, but not a NECESSARY one. It could be just as likely that all of these species were individually affected by the same ERV."
You probably don't need to get into the second part of the paragraph, I believe I can explain that. Just not the first part about species-specification by ERV markers.
I know this was posted quite some time ago, and it's not about ERVs, which I know very little about. But your question brought a paper I recently read to mind. There's a rolling circle transposon, the entire family of which was totally unknown in mammals, and most similar to that of an insect that was found in a bat. My guess is it was in an insect the bat ate and somehow it got into the bat's genome and went crazy.
The point being that these things are not always host specific, and sometimes jump to quite distant relatives.
Pritham, E. J., Feschotte, C., February 2007. Massive amplification of rolling-circle transposons in the lineage of the bat Myotis lucifugus. Proceedings of the National Academy of Sciences of the United States of America 104 (6), 1895-1900.