Knockdown argument for Pseudoscientific anti-evolutionists

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Discussion by: santana navarrette

Endogenous retroviruses (ERVs) are retroviruses (RNA viruses) that infect a hosts nuclear genome, and become integrated  into the genome of an organism. When this infection and integration occurs in the germ line of an organism, this retroviral  insertion will be passed down to the organisms descendents. So, using the theory of evolution, we can predict that 2 species that are descended from common ancestors should share identical ERV insertions, because they would be passed down from their common ancestor. So using this information, and this hypothesis, we can set up an experiment. We know that chimpanzees and humans are very closely related, and that they share a common ancestor. So if we compare the ERV insertions in both of these species genomes, we will see that most, if not all, of their ERV insertions will be identical, which will necessitate common ancestry. 

So, scientists have actually conducted this exact study, and here are the results. 
1) 99.9% of  ERVs in humans, are shared in identical loci (loci=a specific location in a genome) to those in the chimpanzee genome. This means less than 100 of the 200,000 ERVs in humans are lineage specific, and the rest necessitate being passed down from our common ancestor with chimpanzees. 
 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1779541/?report=classic ) 

2) And when the mutations of ERV insertions that are in identical loci are examined, even the mutations on the shared ERVs are found to be identical …and just as with the distribution of ERVs, some shared mutations within a single shared ERV fall into nested hierarchies. (http://www.pnas.org/content/96/18/10254.full) 

To take this data and add a little explanation to it:  
We know how many ERVs Humans and Chimpanzees share for two reasons; examination of indel variation, and whole-genome analysis.  
 
Indels are insertions or deletions to the genome of an organism. When lining up genome sequences for comparison, we can measure the amount of indel variation between the genomes. We can measure this because when multiple specie's genomes are aligned, an indel that only appears in one of the species's genome will result in a gap in the alignment. Whereas indels that are in identical locations, in BOTH specie's genomes, will leave no gaps.  
 
Total indel comparison provides a total number of indels that are shared in identical loci between chimpanzees and humans; but closer examination is necessary to determine how many of the indels in these genomes are ERV insertions, and then even further analysis is needed to find how many of these ERV insertions, are identical in both species. One way this can be done is by isolating only the indels that are the right size to potentially be ERVs. Once this is done, the sequences corresponding to this size can be individually examined and the indels that contain LTRs, pol, env and gag proteins (characteristics found only in viral insertions) are found to be ERVs and are then isolated and examined even further. So after isolating all the ERV indels, we can find the total number of ERVs that are in identical loci by taking the total number of ERVs and subtracting the number of ERVs that form gaps when aligned. After doing this, we find that there are ~200,000 ERVs in the human genome, and that less than ~100 of these ERV indels form gaps when aligned, meaning that more than 99.9% of ERVs in the human genome are identical to ERVs in the Chimpanzee genome, which necessitates common ancestry. 
 
After using indel variations to affirm our initial prediction, we can corroborate the indel variation evidence with genome  wide sequencing (rather than just indel comparison). 
 
In 2005, the available sequence of the Chimpanzee genome was aligned with that of the human genome, and an extensive comparison analysis was performed. As part of this analysis, the researchers looked at every available solo LTR (LTRs are long terminal repeats in the genome which are byproducts of  ERV insertions) and every full-length ERV in the chimpanzee genome, and checked to see if there was also one at each corresponding locus in the Human genome. Just as with the examination of indels variations, the results were that less than ~100 ERVs are human-specific and less than ~300 ERVs are chimpanzee-specific, and the rest were in identical loci, and amazingly, also shared identical mutations as well. (Chimpanzee Sequencing and Analysis Consortium, 2005;R. Waterston, personal communication, April 22, 2010). 


In conclusion, indel variation shows that most indels cannot be lineage-specific; they must be in identical loci. When the indels are further examined, the ERV indels are isolated, and the initial prediction is affirmed, and less than 0.1% of ERVs are found to be lineage-specific, necessitating that the other 99.9% are from our common ancestor with chimpanzees. 

Finally, definitive confirmation is obtained by genome-wide comparison, where virtually all ERVs, and their accompanying LTRs are directly observed to be in identical loci in both genomes. And amazingly, even the mutations in these identical ERVs are found to be identical. 
 
All of this evidence, necessitates humans and chimpanzees to be derived from a common ancestor. 

24 COMMENTS

  1. Your argument is unassailable. Logical, demonstrable, verifiable….. And, sadly, full of things that are “hard”, I sit and shake my head slowly and sadly, because although I KNOW you are dead on right, there is no way that anyone other than a scientist and moreover, a scientist literate in both evolutionary theory AND molecular genetics will digest this. There are many folks here who will love this post and the work that it represents and they will understand it. It is a narrow niche, I am afraid. Popular consumption of this level of science is pretty much never achieved. Even a “science journalist” could screw it up.

    Many creationists will shut down at the first WORD of your post. Way way way over the head of a person who thinks the earth is 6000 years old. I love the tone and passion in the post; but they will shut down immediately because struggling with multisyllabic scientific words is not something they tolerate.

    • In reply to #1 by crookedshoes:

      Your argument is unassailable. Logical, demonstrable, verifiable….. And, sadly, full of things that are “hard”, I sit and shake my head slowly and sadly, because although I KNOW you are dead on right, there is no way that anyone other than a scientist and moreover, a scientist literate in both e…

      I think you could simplify it, though whether or not somebody would accept it is another story. It’s easy for many people to dismiss evidence as some sort of anti-God conspiracy by scientists or something.

      Perhaps one could say something like, “There are viruses that insert their DNA into our DNA, and we end up passing that virus’s DNA sequence to our offspring, generation after generation. If you look in the past, you can see that chimpanzees have the same viral DNA in the exact same place that we do, showing that a common ancestor form a long time ago was infected by this virus.”

      (Please let me know if that’s an oversimplification or just wrong, though.)

      I did once find some argument against this on a Christian website, but I didn’t quite understand what they were arguing, so I wasn’t exactly sure how to refute it. I think they were trying to argue that the viruses were somehow “forced” into inserting DNA into a certain position, so it didn’t reflect a common ancestor at all, but I can’t be sure.

      • In reply to #3 by Kim Probable:
        >

        I think you could simplify it, though whether or not somebody would accept it is another story. It’s easy for many people to dismiss evidence as some sort of anti-God conspiracy by scientists or something.

        Valuable as this is, it is preaching to the choir.
        I don’t think it will make any more impression on creationists than the thousands of other decisive examples of evolution.

        It is at a level which will go straight over the heads of their uneducated followers, giving them the opportunity to make up nonsense which requires scientific education and knowledge in order to understand a refutation. Simplistic believers will be unable to follow. a detailed refutation or the original genetics, so will just choose what they want to believe. That is the way “irreducible complexity” is played to con the ignorant.

        • In reply to #14 by Alan4discussion:

          In reply to #3 by Kim Probable:

          Valuable as this is, it is preaching to the choir.

          Well, I was looking for a way to simplify it for those who wanted to learn, but didn’t have the background for it. I’m always trying to come up with analogies, but want to verify them first.

          People can change, though. I think the bulk of the problem with creationists (I grew up with the evangelical Christian “every other denomination is a false Christian” sort of crowd, so the experiences of others may vary) lies in that they’ve been trained to look for changes in “kinds”. Basically they want to see a cat give birth to a dog or something along those lines. We were taught that of course things change, and you know, Noah probably didn’t bring zebras and horses and asses on board the ark, but one type of horse that later became all of those things. So speciation is generally acceptable, but they’re stuck on that micro-evolution vs macro-evolution thing.

          I made it out, so there’s hope. =) I’ve also seen some people I knew from back then graduate to “thiestic evolution”, which we were taught was a lie from Satan, so they’ve moved on somewhat. Learning that the definition of evolution that I was given in high school / church was not the definition of evolution in the scientific world really broke down a lot of walls for me. I was taught to fear the word itself, but once I had it actually explained, it just made so much sense. Granted, it is still difficult to imagine at times, especially transitional stages, which may hinder some people, but that’s part of what makes it so fascinating to me. Learning how all of that works is wonderful.

    • In reply to #1 by crookedshoes:

      Your argument is unassailable. Logical, demonstrable, verifiable….. And, sadly, full of things that are “hard”, I sit and shake my head slowly and sadly, because although I KNOW you are dead on right, there is no way that anyone other than a scientist and moreover, a scientist literate in both e…

      Not too hard.

      But, evidence not argument. And lot’s of it!!

      ” In conclusion, indel variation shows that most indels cannot be lineage-specific; they must be in identical loci. When the indels are further examined, the ERV indels are isolated, and the initial prediction is affirmed, and less than 0.1% of ERVs are found to be lineage-specific, necessitating that the other 99.9% are from our common ancestor with chimpanzees. “

      This is new to me. Almost 100% of are endogenous retro viral material is shared with our common ancestor Genetically, what happened at that branch point with a viral insertion into a protein code section? In the ” junk? “.

      • Hey, if the virus inserts into a protein coding region, it usually ends with the coding sequence being ruined, then shut down. but the sequence persists from generation to generation. Viruses are lytic or lysogenic and the latter can establish long term relationships within the host’s genome. We’d call this a provirus when it is inserted into the genome. A bunch of our DNA, is, in fact virally acquired.

        The term pseudogene is thrown around to describe a situation where a gene has a mutation or insertion/deletion or even a transposon that destroys it’s function. I’d dare say that this situation with the virus interrupting the coding section of a gene can be thought of as the same type of interruption– the result? a pseudogene.

        I am not sure if this is what you wanted to discuss. But, nonetheless, this is my attempt to start the conversation.

        In reply to #5 by Neodarwinian:

        In reply to #1 by crookedshoes:

        Your argument is unassailable. Logical, demonstrable, verifiable….. And, sadly, full of things that are “hard”, I sit and shake my head slowly and sadly, because although I KNOW you are dead on right, there is no way that anyone other than a scientist and moreove…

        • In reply to #10 by crookedshoes:

          Hey, if the virus inserts into a protein coding region, it usually ends with the coding sequence being ruined, then shut down. but the sequence persists from generation to generation. Viruses are lytic or lysogenic and the latter can establish long term relationships within the host’s genome. We’…

          The shut down of a protein coding region can also ” promote ” evolutionary changes, though those changes are often deleterious in action they might send a population of organisms off in a different evolutionary direction. For an inexact example take vitamin C synthesis in apes ( to keep this restricted ) and there inactivation of that gene as they became primarily fruitivores. So that synthesis gene becomes a pseudogene.

          A lysogenic insertion among the ” junk ” with it’s control regions could be especially interesting as to effect.

          So, any work being done on the evolutionary effect of ERV’s? On any other physiological/behavioral/genetic effects?

          • Great question, none that I know of, but I will poke around… You poke around too. If it’s out there, we can share!

            In reply to #13 by Neodarwinian:

            In reply to #10 by crookedshoes:

            Hey, if the virus inserts into a protein coding region, it usually ends with the coding sequence being ruined, then shut down. but the sequence persists from generation to generation. Viruses are lytic or lysogenic and the latter can establish long term relationsh…

          • In reply to #17 by crookedshoes:

            Great question, none that I know of, but I will poke around… You poke around too. If it’s out there, we can share!

            In reply to #13 by Neodarwinian:

            In reply to #10 by crookedshoes:

            Hey, if the virus inserts into a protein coding region, it usually ends with the coding sequence being ruined, th…

            Will do.

            http://www.askabiologist.org.uk/answers/viewtopic.php?id=8262

            A tantalizing little something although the internet comes up thin here. I always thought these ERV’s could be more than taxonomic markers.

  2. First, can this topic be edited to remove the hard returns?(mods?) It was obviously written in another program and copied it into the post block causing the returns to be visible. It would require deleting the space at each hard return.

    I hope several knowledgeable people will expand on this excellent topic. I unfortunately cannot. I share crookedshoes’ opinion; I hope we can move past any issue of the article being too complex for most creationists and allow those educated on the matter to contribute additional information and views.

    crookedshoes, I was thinking the same thing as I was reading this article and trying to find a way around the obvious issue of its complexity.

    As someone who accepts Evolution and is scientifically illiterate, I can barely grasp this fully. I start to lose it after the second or so paragraph. Imagine a creationist that accepts an explanation that’s a few pages long. So here’s a few ideas. 1. print out this article and show it to someone who does not accept Evolution. When they complain that it is too complex. Thank them for being honest that they are not comprehending the information. Ask them if they could now be honest with themselves that they are not as knowledgeable about various issues they they have taken for granted. Knowledge is built upon. Being unable to fully understand this information requires beginning with a base knowledge. Let them know that this is one piece of information is amongst miles long studies of various aspects of Evolution. Reassure them that it’s OK to admit that they are not fully educated on a topic and should avoid making decisions without being better informed. 2.Find a way to simplify the information through illustrations or dumbing it down. “Tell it to them like they are ten year olds.”

  3. Thanks Quine, I found some Utube videos that really helped explain the information. I especially liked this one: http://www.youtube.com/watch?v=qh7OclPDN_s The part about the cats is quite interesting (meow)

    I also found “debunking” information and thought I would set the stage for someone to comment. Here are a few challenges.

    1. ERVs are not a product of retroviruses.
    2. Apoptosis should have rid retroviruses (“viral infected” EVRs) long ago.
    3. ERVs can move around. Only 14 of 98,000 are located in the same area as chimps.
    4. ERVs are really retroviral promoters or switches in human genome.
    5. ERVs should not have function, but ERVs do.

    Thank you for this topic, I am eager to hear a response since I’m CuriousKat today and find this information fascinating.

  4. ” In conclusion, indel variation shows that most indels cannot be lineage-specific; they must be in identical loci. When the indels are further examined, the ERV indels are isolated, and the initial prediction is affirmed, and less than 0.1% of ERVs are found to be lineage-specific, necessitating that the other 99.9% are from our common ancestor with chimpanzees. ”
    This is new to me. Almost 100% of are endogenous retro viral material is shared with our common ancestor Genetically, what happened at that branch point with a viral insertion into a protein code section? In the ” junk? “.

    I learned a little today. Refreshed my screen to read this and realized I still know nothing. Maybe tomorrow?

  5. This argument is evidence to an anti-evolutionist, but only regarding what foolish scientists might misinterpret as meaning that evolution has occurred. It isn’t convincing evidence about how evolution might occur.

    Creationists’ arguments routinely allow for the appearance of evolutionary artifacts like this. Any creator worth having should be able to generate whatever artifacts serve its unknowable purpose (maybe to tempt potentially evil scientists), as well as being able to produce life from nothing, with nervous impulses, thoughts, memories, already in process, and circulating blood already in effect and up to normal blood pressure. (Not to mention light miraculously created already originating in transmission from distant multibillion year old galaxies and so able to be received in telescopes in only a few thousand years time on Earth. Or to create women from a man’s rib etc.)

    This research is not really a knockdown argument because most anti-evolutionists aren’t really across the demarcation of science vs pseudoscience. Possibly many actual scientists aren’t even fully across the demarcation issue. Plus anti-evolutionists have already accumulated plenty of evidence about how scientists occasionally lie about these kinds of things. (E.g. Richard Dawkins’ interview being prima facie evidence proving his inability to explain information content of genomes etc.)

    But, as Crookedshoes points out, the OP argument is too complex, requiring too much assumed comprehension of the mechanisms of molecular biology and genetics. Something that creation science has proved is simply not necessary and not worth the effort to comprehend. A useful explanation needs to be more in the realms of how Noah was able to handle effluent disposal on the ark.

    A real knockdown argument is an actual punch in the face. Claiming, however credibly, to be capable of a successful king hit to the head is always trumped by an actual king hit. King hits are now an increasingly fashionable and popular sport in Sydney Australia, with the potential even to exceed the popularity of glassing and drive byes, and now apparently being subsidised by various judicial incentives – e.g. $500 fine for an unlicensed person possessing and threatening someone with an illegally imported loaded pistol. (Most such fines being paid for directly by government welfare on the basis of financial hardship to the dependent person.) Or only 4 years prison for king hit killing someone at random for entertainment. Many people, like members of the judiciary, are too removed from reality and too ill-informed to take real threats seriously, however credible such threats may be to the fully informed.

    If anyone can assist, I’m looking for an genuinely credible argument. (Credible to reasonably intelligent anti-evolutionists.) Something that isn’t too technical, but that demonstrates the underlying molecular basis of evolutionary changes. Not just evidence of species similarity and common descent, but evidence of actual gene modifications via mutations generating novel protein combinations with significant observable impact on processes and potential exposure to selection pressure and heritability. I’m sure there’s stuff out there – probably not spectacular though. Mundane plant breeding programs in agriculture or bacterial studies etc.

    Please let me know of anything like this.

    Anti-evolutionists aren’t stupid. Some of them will welcome an argument that disposes of a potentially frivolous objection to evolution. The idea being that this should enable them to focus more on the real issues of why evolution really is not true.

  6. Don’t be silly. There is probably not a creationist on earth who could understand your argument. If they did, they would not trust themselves to be persuaded by it.

    We keep coming up with arguments that would be conclusive for each other. But they are just meaningless technobabble to creationists who have at most a second grade science education.

    At some point we have to study the glue that holds christian balderdash in place, and come up with arguments specifically targeted to dissolve that glue.

    I suspect most defections occur when people become convinced god as abandoned them than when they become convinced he does not exist.

  7. Thank you for your excellent and informative post.

    Unfortunately I believe that we are fighting a losing battle here. For every unassailable argument that real scientists come up with, a creation “scientist” will have a rebuttal. The speed of light is not universally constant, they will say, or radioactive decay rates have changed over time and so on. Their arguments are hogwash but they posess two important (to them) qualities:

    1) they are not testable, and
    2) they have the aura of validity; they sound, to the ears of thier target audience, as if they make sense and are based on scientific principles.

    Their aim is to promote, in the minds of the simple, the idea that there is an equivalence between Darwinism on the one hand and Creationism on the other. As we know, there is no such thing. But how to convince people of that? Sadly I think we cannot.

  8. I’d be lying if I said I understood even 50% of your post. But I got the gist of it and am now furiously researching the rest of it to manage an acceptable grasp of your argument. Like crookedshoes said, it’s hard, but with your permission I’d like to share this in print and with some extra information with a few of my friends and colleagues.

  9. 14 Alan4discussion #15 Kim Probable

    I was just thinking along those lines when planning to comment to @jbjb on another thread. I was going to suggest that he do some groundwork first, before leaping into really difficult areas. If suddenly confronted with extremely complex concepts it’s all to easy to slip back into the simple answers presented by creationism.

    • I’d just like to piggyback and add that the illusion of design is a strong illusion. Seeing through it requires knowledge, an open mind, and often a step back to see a big picture. Structure/function relationships often lead to conclusions of design, however, evolution yields compromises and leaves it’s footprint. You gotta look!

      In reply to #16 by Nitya:

      14 Alan4discussion #15 Kim Probable

      I was just thinking along those lines when planning to comment to @jbjb on another thread. I was going to suggest that he do some groundwork first, before leaping into really difficult areas. If suddenly confronted with extremely complex concepts it’s all to easy…

      • In reply to #18 by crookedshoes:

        I’d just like to piggyback and add that the illusion of design is a strong illusion. Seeing through it requires knowledge, an open mind, and often a step back to see a big picture. Structure/function relationships often lead to conclusions of design, however, evolution yields compromises and leave…

        I hope that jbjb doesn’t read this thread looking for answers that are going to prove it for him one way or another. Bewildering for me!

  10. Great data, but it would be made all the stronger with a cladistic analysis that included other mammalian, or even vertebrate taxa, demonstrating apomorphies and branch points in a proposed cladogram. As it stands its just a phenetic analysis, a long defunct phylogenetic concept. To explain, the study fails to demonstrate that the ERV characters that humans share with chimpanzees are unique to that clade (lineage if you like). They might be, but it doesn’t demonstrate it by out group comparison.

  11. I got the gist of this, but then I have a background in biology. It may be useful for those creationist sophists who try to use more sophisticated pseudoscientific arguments than your average Ken Ham fan, but I agree it would zoom miles over the heads of people who think Ray Comfort nailed it with his banana. Once, while trying to demonstrate the irrefutable fact that we are apes to a creationist, I tried to make it short and simple. I said, “Chimps and humans are about 98% the same genetically. If I gave you a sandwich that was 98% shit and 2% ham, would you still call it a ham sandwich?”

  12. Beautiful post for the technically literate but I doubt it’s going to knock many creationists down. I’ll echo many previous comments by suggesting that it’s both too technical and contrary to creationist dogma.

    The technical details could be reduced and simplified which could easily make this an extremely useful argument for non-creationists or lapsed/questioning creationists who don’t have their heads buried firmly in the sand. To a thinking mind it gets a little difficult to argue that Gawd Olmighty gave us and the chimps an overwhelming majority of genetic errors in exactly the same positions for no good reason. It would also be a handy piece of ammo for people to use at such venues as the Kansas school boards, etc.

    The truly insurmountable hurdle is that diehard creationists have no use for science except when it agrees with their religion. Anybody who can conceive of a 13.7 billion light-year universe in a 6017 year bottle, accelerate continental drift to highway speeds and alter fundamental universal constants to suit their own mythology will have no problem ignoring your pesky ERVs. These people don’t respond to reason and an entirely different approach is required.

    I’m honestly much more interested in the continued scientific applications. Although I don’t understand all the technical aspects, ERVs look like they could be an extremely powerful tool for molecular cladistics. Given that we’re seeing 99.9% correspondence some 5 to 7 Ma after the human-chimp last common ancestor suggests that ERVs are durable genetic markers over moderate to long timescales. Would you consider sparking up an off-shoot post in the “Science” forums to discuss? Are you aware of any comparisons with any of our more distant primate relatives?

  13. How about this?-

    It would of course be wrong to claim that birds and bats are descended from a common, recent ancestor because they both fly. Flying is a general solution to the problem of staying alive which has been independently arrived at by birds and by bats. Shared DNA sequences might be no more indicative, because they might just be the result of the same molecular solution to a shared problem.

    In the same way, it is not enough to say that chimpanzees and humans are descended from a recent common ancestor because of some observed similarities, like the shape of the ears, or similar bits of DNA, although the number and closeness of similarities is very great. However, there are certain sequences of molecules found in the DNA of both chimpanzees and humans which could only have got into their genes through a common ancestor. The reasons are as follows:

    1. It is known that viruses act by hijacking the reproductive machinery of cells in the host, inserting their own DNA fragments into the host DNA. Many of these insertions have no ill-effect in terms of the health of the host and certain of them can be passed on to the host’s offspring. Insertions of this type are very common, and there are many thousands in the DNA of chimpanzees, humans, rats and oak trees, which go completely unnoticed, and which are passed on from parents to offspring. One type of insertion is called ERV because it is the result of Endogenous Retro Viruses, but this not important to the argument.

    2. Humans and chimpanzees who are today exposed to ERVs could be infected, without suffering any kind of illness, and by examining the DNA, it would be possible to state which ERV was responsible for some particular insertion discovered. On its own, that would only tell us that some chimpanzees and some humans happened to be out and about when a certain ERV was around and that some individuals of each species were separately infected.

    3. However, ERV insertions can occur at many different places, called loci, in the very long molecule of DNA and the loci are preserved when the hosts reproduce. If the ERV infections are independent, then they will almost certainly turn up in different loci, and this is observed if two individuals or two different species are infected with identical ERVs. The loci of each ERV infection are unique. Only if the ERV infection occurs in a common ancestor do the insertions turn up in the same place on the DNA of each of the offspring. And this is observed: a massive 99.9% of the 200,000 or so ERV insertions in chimpanzees and in humans have the same loci.

    The only reasonable conclusion is that it was our common ancestor that was infected with these ERVs, and that we have inherited not only the DNA fragments which identify the ERVs responsible but the particular loci, fixed at the moment of infection and transmitted through the common ancestor of the two different species.

    This would be a bit like finding the name of the same factory stamped on the metal parts of two different aircraft, one a Boeing and one an Airbus. We would know that there was a common origin.

    Bill Dixon

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