Facts Of Evolution: Retroviruses And Pseudogenes

Pronunciation of 'genome': I normally hear 'gene-ome', not, the way the person in this video pronounced it, 'genn-ome'. Do you know whether there is a preferred or most common pronunciation of this word, or is this one of those science words that gets said multiple ways, or is the narrator of this video unfamiliar with the word?

I am glad you liked this too. When I first saw it, I wondered if he got his information from you, Abbie :)

Very cool.

Q: Do erv's have some kind of self-correction or maintenance system? If not, how far up/across the tree can you look before mutations make erv's unrecognizable as related? Is there a way to tell recent duplication insertion from recent re-infection?

Nice video, I found some of the graphics distracting, but a great message.

Too bad the religitards will find their delusions too distracting to get anything from this.

Excellent vid. My only criticism would be that the guy ... talks ... far ... too ... slow - ly. :^)

Is it politically correct to show monkeys, black people and asian people as branches on a mythological evolutionary tree? (5:00)

Regarding Ivan's comment about speaking too slowly, you have to consider the audience and the topic.

My god, couldn't he have a found an actual Australian aboriginal to illustrate the Australian population? Why use a Han phenotype? And the ancestral primate lacks a tail, so it must be an ape, not a general primate. The ersatz taxonomic Latin sucks too. And "jinome"? "phylogenic"?

Apart from that, great video.

I suspect they didn't use a picture of an aborigine for a couple of good reasons:(1) They wanted to emphasise that it was an arbitrary example, and (2) some Aus aborignal cultures have sensitivities around displaying pictures of people, particularly people who are dead. - it was just a clumsy step around a minefield.
;;
Presumably it's possible for these genetic markers to be overwritten, but the statistical arguments to show that the inference of common descent is still valid would have overcomplicated the video - yes?

William Wallace -

Is it politically correct to show monkeys, black people and asian people as branches on a mythological evolutionary tree? (5:00)

Yes. The bigotry you imply is merely a projection. A European looking face was also used.

Regarding Ivan's comment about speaking too slowly, you have to consider the audience and the topic.

Trying to cover your ignorance with nastiness again, William Wallace?

Well, who knows. Perhaps you have a valid critique of the video. To make one, you would have to have understood the basic concepts. An important logical requirement, prior to disputing someone else's arguments, is to understand what they are saying. Let's test that. Please feel free to watch the video over and over again and quote directly from it.

1) Can you explain, in specific terms, the concept of an ERV, as explained in the video?

2) Can you explain why scientists view ERVs as (one of many lines of) evidence for common descent? Not whether or not you agree or what you believe. Just a fair statement of the argument of those who do so view them.

Harold,

You're a f*cking idiot. As is typical among evolanders, you make assumptions, and if those assumptions fit your preconceived ideas, you believe that is the same as being true. I made the following in 2009: http://blog.coincidencetheories.com/img/erv1.gif Take a look, and critic. I've also read "Differences in HERV-K LTR insertions in orthologous loci of humans and great apes" by Lebedev et. al,as well as "Full-sized HERV-K (HML-2) human endogenous retroviral LTR sequences on human chromosome 21: map locations and evolutionary history" by Kurdyukov et. al. If you have any more recent papers you'd like to recommend, I am more than willing to read them and offer my thoughts.

The problem with ERVs in support of common descent is the experiment is *not* a scientific test of common descent. If the ERVs in question had never been found, or, if all of the genomes were entirely mapped, and other ERVs were found that did not support the accepted phylogenetic tree, common descent would not be falsified. This is key to understanding this video, and similar arguments made by evolanders.

My conclusion is that the argument that ERVs prove common descent is propaganda, not science. Even Abbie and many of her followers seem to agree with, but she and others continue to spew misleading propaganda such as this video.

At best, phylogenetic trees are evidence of common descent. But in the video, and evolanders in general, confuse evidence and proof when it is convenient for them.

Evolanders understand falsifiability enough to be careful not to make many falsifiable claims, such as "If you ever found an ERV that went against the accepted phylogenetic tree, then common descent of humans and great apes would be falsified."

Now, if there were such a claim, the video would be much more interesting. As it is now, the video is propaganda geared toward people with an IQ of 105-115, and ERVs are mere fodder in the propaganda war between evolanders and creationists.

Willy, you might want to understand the difference between "Falsification of common descent" and "Falsification of a specific phylogenetic tree" before you lecture anybody on logic. For example, until a couple of decades ago most biologists expected that our closest relatives among the great apes would be gorillas. Once we got genetic data, it turned out that our closest relatives are the chimps. Genetic data falsified one proposed phylogenetic tree [[Human, Gorilla], chimp] and supported a different tree [[Human, chimp], Gorilla]. In both trees, however, all three lifeforms have common descent, and this is supported by the genetic data; absent common descent there's no reason for such close genetic similarities at all.

William Wallace -

You were not willing or able to answer my questions. However, I will address your post, in order to show to others why you are wrong.

You're a f*cking idiot. As is typical among evolanders, you make assumptions, and if those assumptions fit your preconceived ideas, you believe that is the same as being true.

Not supported by the evidence, and irrelevant if it were supported by the evidence.

I made the following in 2009: http://blog.coincidencetheories.com/img/erv1.gif Take a look, and critic.

The link opens to a table summarizing some erv data, which you label as "coincidence".

I've also read "Differences in HERV-K LTR insertions in orthologous loci of humans and great apes" by Lebedev et. al,as well as "Full-sized HERV-K (HML-2) human endogenous retroviral LTR sequences on human chromosome 21: map locations and evolutionary history" by Kurdyukov et. al. If you have any more recent papers you'd like to recommend, I am more than willing to read them and offer my thoughts.

Simply listing the title of a paper is irrelevant.

The problem with ERVs in support of common descent is the experiment is *not* a scientific test of common descent. If the ERVs in question had never been found, or, if all of the genomes were entirely mapped, and other ERVs were found that did not support the accepted phylogenetic tree, common descent would not be falsified.

Incorrect. ERV data is one test of both phyologenetic relationships, and the general concept of common descent.

It is true that, if ERV data were incompatible with all of the other evidence for common descent and the phyolegenies it demonstrates, that alone would not "disprove" common descent. Proof is for mathematics.

However, it would be a very major challenge. The theory of evolution predicts that new discoveries will be consistent with common descent and reasonable phylogenies.

There have been many opportunities for such challenges to arise. Biochemistry - but all life shares common biochemistry. Classical genetics - but classical genetics is consistent with the theory of evolution. Cell biology - but life shares common cellular structures. Molecular biology - but all life shares a common biochemistry of genetics and a common genetic code.

Each new discovery could have challenged common descent, but instead, each new discovery has been compatible with common descent.

This is key to understanding this video, and similar arguments made by evolanders.

My conclusion is that the argument that ERVs prove common descent is propaganda, not science. Even Abbie and many of her followers seem to agree with, but she and others continue to spew misleading propaganda such as this video.

No-one made the argument that ERVs alone "prove" common descent. Proof is for mathematics.

The argument is that the distribution of ERVs is as would be predicted by common descent and phylogenies already known from other evidence.

At best, phylogenetic trees are evidence of common descent. But in the video, and evolanders in general, confuse evidence and proof when it is convenient for them.

"Proof" is for mathematics. Data that supports phyologentic trees is one line of evidence for common descent.

Evolanders understand falsifiability enough to be careful not to make many falsifiable claims, such as "If you ever found an ERV that went against the accepted phylogenetic tree, then common descent of humans and great apes would be falsified."

Such a finding would be a major challenge and would require an explanation. There are too many other lines of evidence for recent common descent for great apes and humans for one single challenge to immediately invalidate all the other evidence. But a "wrong" distribution of ERVs would be a major challenge.

Now, if there were such a claim, the video would be much more interesting. As it is now, the video is propaganda geared toward people with an IQ of 105-115, and ERVs are mere fodder in the propaganda war between evolanders and creationists.

The only propaganda war is being waged by creationists.

ERV data fulfills the prediction that new data will be consistent with common descent and reasonable phylogenies. It is an obvious line of evidence in favor of common descent.

William Wallace -

A few threads ago I asked you what credentials you had in computer science, in a verifiable way, and to demonstrate with a few lines of code.

The reason I asked was that you implied expertise.

Of course, a satisfactory answer wouldn't change the quality of your arguments on the topic at hand.

But an unsatisfactory answer casts doubt on your overall credibility.

I went back to that thread, and I was left with doubts.

You provided a very, very trivial demonstration of "writing code". You stated that it was "written by a PhD in computer science". That does not even amount to a statement that you have such a PhD, let alone a verifiable one.

You provided some utterly irrelevant links to the movie Good Will Hunting.

You then got into a trivial discussion with someone else about Soduko.

I would just like to make note of the fact that you were unwilling or psychologically unable to give an honest answer there.

Likewise, here, the only thing I really asked you to do was to state a fair understanding of the claims made in the video, BEFORE arguing against them. You weren't able to.

If you are operating under the illusion that you are "genius" of some sort I will note that -

1) High innate ability does not amount to expertise in a field in which you are ignorant. An ignorant genius is still an ignoramus.

2) You seem to be unable or unwilling to argue logically, at least on the topic of this thread. Perhaps you are a genius, but impeded from discussing the topic at hand logically by emotional bias. An emotional bias that completely prevents logical thought on a particular topic would, of course, entirely negate any advantage that "genius" or "high IQ" might otherwise bring to the table.

Regarding falsification of a particular tree

Genetic data falsified one proposed phylogenetic tree [[Human, Gorilla], chimp] and supported a different tree [[Human, chimp], Gorilla].

Was this based in whole or in part on ERVs? If so, interesting.

You provided a very, very trivial demonstration of "writing code". You stated that it was "written by a PhD in computer science". That does not even amount to a statement that you have such a PhD, let alone a verifiable one.

From the other post:

Written by a Ph.D. computer scientist:

int main(int argc, char** argv) {
for (int c = getchar(); c != -1; c = getchar()) {}
c = c & 170;
putchar(c);
}
}
Let me know what you think.

That scrap of code came from Mark Chu-Carroll of the Good Math, Bad Math blog. Unless he's Mark, he didn't write it.

http://scienceblogs.com/goodmath/2009/04/the_return_of_the_compression…

Bah. Blockquote fail. Second blockquote should have been after the "Let me know what you think." line.

@14: the initial conclusion was based on whole-genome similarity from pairing tests; subsequently it's been backed up by whole-genome sequencing (the draft of the chimp genome was in Nature in 2005); and the ERVs tell the same story, e.g. Polavarapu N, Bowen NJ, McDonald JF. Identification, characterization and comparative genomics of chimpanzee endogenous retroviruses. Genome Biol. 2006;7(6):R51.

You should really do some reading yourself before expressing opinions.

#15, and it doesn't even compile. LOL.

Kemanorel, also, I was going to let you bow out gracefully, but since you seem to have so much time on your hands, when are you going to get that sudoku puzzle solved with your piece of sh*t attempt at a solution?

William Wallace -

1) No-one challenged Kemanorel's honesty.

2) In the unlikely event that Kemanorel is a bad programmer, life still evolves, and I still suspect YOU of being a liar.

3) Even if you're not a liar, life still evolves. But still, if you don't want everybody to think you're a liar, you should STFU about Kemanorel and sudoku, and show that you have the comp sci credentials that YOU implied. Please do so.

Where did I ever claim or even imply that it was my code. It was a response to a request for a snippet of code I claim expertise in, not a request for code that I wrote. I provided a snippet of code, and accurately identified it as being written by a Ph.D. computer scientist.

Worse, it doesn't even compile, which you were also incapable of seeing.

ERV fanboys are truly laughable.

Stephen Wells (#17) I'll take a look at "Identification, characterization and comparative genomics of chimpanzee endogenous retroviruses"

Harold (#20), I was foolishly asked to provide in another thread a snippet of code that I claim expertise in. I claim expertise in C, among other computer languages. I was not asked for a snippet of code that I wrote. I did not provide such a snippet. I identified the author as being a Ph.D. computer scientist. Mark Chu-Carroll, to the best of my knowledge, is a Ph.D. computer scientist. I selected the code as a hybrid practical joke/social experiment. I wanted to see if the words "Ph.D. computer scientist" would render you all too stupid to see the obvious error in the code, or if you incorrectly think it was my code, and then mock me for the obvious error once discovered. It was a poorly conceived social experiment, however, because, while the error was not identified, I don't know if it is because you were hypnotized by the phrase "Ph.D. computer scientist" or just too stupid to see the error.

Regarding the Good Will Hunting clips (#13). I think you missed the point. The point is not that I am a genius (if I were, why would I spend my time arguing with ERV fanboys?); the point was to shed light on the silliness in ERV fanboy's fascination with credentials, as if my observation that recent computer scientist graduates are less competent than their forerunners would be rendered worthless if I didn't earn an computer science degree at MIT. A degree one has and the correctness of one's observations are orthogonal to each other.

I think the point, Willy Walrus, is that you have demonstrated yourself to be a moron. To bad you weren't in my class back in the day, I would have derived great pleasure from flunking your punk ass.

You sell insurance now, right?

Uh, judging by the fact that the "include" preprocessor was left empty in the original, I doubt it was actually intended to compile, Wallaids. Perhaps you never learned how to write pseudocode in your CS classes, once again highlighting your mediocrity.

2) In the unlikely event that Kemanorel is a bad programmer, life still evolves, and I still suspect YOU of being a liar.

Thanks for that, Harold.

Uh, judging by the fact that the "include" preprocessor was left empty in the original, I doubt it was actually intended to compile, Wallaids.

Exactly right. That code snippet is short hand for PART of a script.

Coders use short hand like this:

while( x = getchar() != EOF)

Which won't compile, but a computer programmer familiar with C/Java, because it's much faster than writing out this to mean the same thing:

x = getchar();
while( x != fin.EOF()) //fin is a file instream
{
...
x = getchar();
}

The fact WW didn't recognize that tells a LOT about his coding ability.

I commented at length about WW not understanding short hand on the other post, and giving a much more detailed account of my own coding ability by posting examples from my AI "Push" game. I just hope ERV indulges the length because it fell into moderation because of it.

To[sic] bad you weren't in my class back in the day, I would have derived great pleasure from flunking your punk ass.

You sell insurance now, right?--Doc Bill

No, I don't sell insurance.

But they let you teach? Pray tell, where?

Damnit Wallace, this is a temp agency, not a research facility! CS stands for Custodial Services. This is the fourth time this year I've had an irate client call and complain about how you sent a computer geek when he wanted a janitor to sweep the parking lot.

Don't forget to also look at the chimpanzee genome project and the human/chimpanzee chromosome alignments, so you can get a proper sense of how deep the genetic similarities are, how consistent the different kinds of genetic test are, and how pitifully underinformed you are.

William Wallace writes:

I wanted to see if the words "Ph.D. computer scientist" would render you all too stupid to see the obvious error in the code, or if you incorrectly think it was my code, and then mock me for the obvious error once discovered.

How fiendishly clever of you. BTW, you left out the "BWAHAHAHAHA!" at the end.

I wanted to see if the words "Ph.D. computer scientist" would render you all too stupid to see the obvious error in the code, or if you incorrectly think it was my code, and then mock me for the obvious error once discovered.

Of course, we all chose option c) probable plagiarism. Once plagiarism was proven, there was no need to examine the code, as it wouldn't demonstrate anything re: Billy Ball-less's competence.

Screw it, since you have better things to do, I'll just tell you the answer: {}.
...
To[sic] bad you weren't in my class back in the day, I would have derived great pleasure from flunking your punk ass.

Okay, you've convinced us, Wee Willy Wanker. You have excellent copy-editing skills. The challenge, however, was to demonstrate coding skills. Oh wait, he's a creationist, quotemining is one of their fortes. He must have thought he was being asked to demonstrate his co(py-e)d(it)ing skills.

Come to think on it, the Limpster was bragging this time last year about having created a program that showed that ERVs aren't evidence for common descent. I challenged him on it, and although he initially gave me some incredibly vague descriptions of his program, he bravely ran away when I started pressing for details. I assumed cowardice at the time - maybe he never had a program in the first place. Hmmm...

Come to think on it, the Limpster was bragging this time last year about having created a program that showed that ERVs aren't evidence for common descent... maybe he never had a program in the first place.

There's no way he wrote a program to do sequence alignment.

Not only do I doubt is programming skill, but I doubt his ability to correctly write a program that would take into account the domain structure and 3-D structures of the sequences he's supposed to be aligning for similarity computation.

But assuming he wrote the program and understood it correctly, then I doubt his ability to interpret the results correctly if he's saying ERVs aren't evidence.

I doubt his ability to know whether he should be aligning nucleotides, proteins, DNA to proteins, or proteins to translated DNA.

I also doubt his ability to even know the difference between a global alignment and a local one.

Kemanorel-

Actually, that's not the tack he was taking. He was basically arguing that multiple, independent, random insertions would give the same pattern as the standard ERV common descent model (in which there is a single insertion, followed by multiple copying events spread out over geological-scale time). You can see my analysis as my most 'recent' blog entry (click my name). Scare quotes because I've been too busy to update the blog for the last 11 months (I moved, and am just now finishing unpacking). It has some links to the beginning of the discussion, but I forgot to link to the revival of that discussion for some reason.

Aagh, moderation hell. Kem, my last post may not appear for a while, so click on my name on my previous post if you want to see what Willy was trying to model last year.

He was basically arguing that multiple, independent, random insertions would give the same pattern as the standard ERV common descent model (in which there is a single insertion, followed by multiple copying events spread out over geological-scale time).

Heh. No amount of programming skill is going to fix a premise that flawed. Even the best programmer in the world would never be able to make an accurate representation of the system based on that.

To be fair, I have vastly oversimplified his argument. Then again, his argument was based on a vast oversimplification of what we mean by ERVs being strong evidence for common descent. In essence, he was ignoring all of the data that goes into showing that ERVs are homologous, not to mention ignoring in situ phylogenies for homologous ERVs.

His argument, as I understood it:

Given x species and y numbered ERVs, each species will have anywhere from 0-y ERVs. This can be represented with an ID hash, with each ERV being assigned a corresponding bit. Use a pRNG to generate an integer between 0 and y^2-1 to represent the simplified genome of each species. The simplified genome of each species would then indicate, by the pattern of 0s and 1s, which ERVs the species has. Run this enough times, and a subset of these randomly generated genomes will show what appears to be a nested hierarchy.

Of course, Wally is stacking the deck even further - he's only using a subset of the ERV data. A single family of ERVs (and dated data at that), and only a handful of species.

To be fair, I have vastly oversimplified his argument.

True, but his premises on the other site about a geometric population growth and such render his model to be nothing more than noise anyways.

His model also wouldn't account for the recently found BDVs either. It's a moot point though because he's already known to be a kook.

challenged him on it, and although he initially gave me some incredibly vague descriptions of his program, he bravely ran away when I started pressing for details. I assumed cowardice at the time - maybe he never had a program in the first place. Hmmm...

He sure doesn't have much in common with that other William Wallace, does he? http://en.wikipedia.org/wiki/William_Wallace

WKV, you description is wrong in details, but your critique that the model used may not match the best known model is fair. Your assertion that the results are unsurprising was what I was saying from the very beginning. However, the point was:

1. ERVs generated using a pseudo-random process as a model for a stochastic process, if searched backwards, could possibly support common descent even if the species considered were specially created (e.g., not descended from a common ancestor). By varying the range of random numbers, such a stochastic process was found to support common descent even when the modeled species were "specially created".

Now, my understanding, and correct me if I am wrong, is that the ERVs that were found to support common descent were sought. They were not accidentally discovered after fully mapping out all of the relevante genomes. Correct me if I am wrong.

On an aside, some ask why would a creator copy mistakes (ERVs). On this, Kemanorel's reuse of his own code is an interesting example. Of course this tantamount to comparing the a creator with a disgraced programmer, but anyway...the possibility also exists that ERVs with no known function actually have a latent function not yet understood by biologists.

Furthermore, I don't recall ever claiming that the model used is how ERVs are distributed in genomes. The model was a premise, and the above conclusion followed from the premise.

If you have a better quality model, please describe it mathematically, or point to a paper published in peer reviewed journal that describes it mathematically, and I will see what happens under that model, using two simulations, one with, and the other without, common descent. Of course, the model used without common descent will likely produce different results unless modified, but by varying the model used for specially created species, and seeing if similar results can be obtained, it may lead to alternative explanations currently dismissed by those mathematical super geniuses otherwise known as biologists.

The model you point me to better produce at least as many ERVs as are currently known.

But my guess is no such model exists. I'd love to be wrong on this, though.

WKV, you description is wrong in details,

I asked, you ran. Feel free to enlighten me.

your critique that the model used may not match the best known model is fair.

That wasn't my critique - my critique is that your model was oversimplified to the point of irrelevancy. You only analyzed 14 of about 98,000 ERVs.

Now, my understanding, and correct me if I am wrong, is that the ERVs that were found to support common descent were sought. They were not accidentally discovered after fully mapping out all of the relevante genomes. Correct me if I am wrong.

You are right. You are also wrong. Some of the ERVs were sought. Some were accidentally discovered. Not all ERVs are 'created' equal. There are a few dozen nearly complete ERVs in a genome. These were large enough and distinct enough to be discovered before full-genome mapping. In 1989, phylogenies of these types of ERVs were created, which matched existing phylogenies. As our technology improved, more ERVs were discovered, which prompted us to go out and look at other genomes to see if the new phylogenies still matched up. Which they did. Wash, rinse, repeat.

If you have a better quality model, please describe it mathematically

Here's a quick stab.

Assumptions: genome size is ~3,000,000,000 bp, the average ERV is ~2,400 bp, and a normal distribution of ERVs. This gives us 1,250,000 segments. If we set the probability that a given segment is an ERV to 8% (which is the percentage of the human genome that is made of ERVs), we should get roughly 100,000 ERVs in a genome. Now, let's add a twist. Let's make 90% of these ERVs Type 1, 9.95% Type 2, and 0.05% Type 3.

Data structure: each genome will be 2,500,000 bits long (about 305 KB). Each segment is two bits. A 00 means no ERV (~1,150,000 total), a 01 is a Type 1 ERV (~90,000 total), a 10 is a Type 2 ERV (~9,950 total), and a 11 is a Type 3 ERV (~50 total). Let's make 10 genomes per run. Total data storage required per run: 3 MB.

Analysis: Obviously, comparing such a large file is processor heavy, to say the least. So we're going to spot check. Select a reference genome. Randomly select 14 of the roughly 50 Type 3 ERVs. Compare these 14 ERVs to the same segments in the other 9 genomes and create a phylogeny, keeping track of ERV types (keeping in mind that 3s degrade into 2s and 1s, and 2s degrade into 1s). Next, take 14 Type 2 ERVs from the reference genome and generate a phylogeny. Finally, take 14 Type 1 ERVs and generate a phylogeny.

Now, do these 3 phylogenies substantially match the phylogeny you created before you started? Oh, I forgot to mention that little tidbit, didn't I?

Have fun!

Oh, btw, not only do the locations make a nested hierarchy in the common descent model, but the actual sequences do as well. But we've simplified it for you.

You may want to read this before you go and say pseudogenes prove evolution.

http://discovermagazine.com/2003/sep/breakgene

Enjoyed reading
TY

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Wouldn't the ERV DNA simply indicate that those creatures found with it were all equally susceptible to the virus? Their ancestors could have co-existed when the virus was active.

Perhaps all of the "pseudo genes" contain a message.