Before we move on to PTERV insetions, do you agree that they lied about the number of orthologous ERV's?
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Endogenous Retroviruses: Evidence for Human Evolution
- Thread starter Loudmouth
- Start date
Before we move on to PTERV insetions, do you agree that they lied about the number of orthologous ERV's?
Some more fun with the lying creationist rebuttal.
Do Shared ERVs Support Common Ancestry? - Evolution News & Views
They try to insinuate that retroviral locus-specific site preference can result in the pattern of ERV's shared by humans and chimps. Of course, they try to claim that just 12 out of "tens of thousands" are orthologous, so obviously their argument falls apart right away. However, it is worth the time to sweep up the other nonsense they have in their "article".
They cite a paper by Sverdlov paper that itself references this paper:
Distribution of targets for avian retrovirus DNA integration in vivo.
In the real scientific paper, the authors state that one of their integration sites saw a rate of integration 280 times higher than what would be expected from purely random insertion. So what does that really mean? From the paper:
"In all experiments, estimates of the m.o.i. ranged from two to three integrated proviruses per cell. A pool of 10 ug of infected TEF DNA (from -5x 10^6 cells) would therefore contain ~1-1.5 x 10^7 integration events. If integration occurred at random throughout the gehome (size 2x 10^9 bp) we would expect to see about two to three integrations, in each orientation, within the 500-bp stretch of DNA analyzed in each reaction."
So, out of 10 million integrations, they would expect 3 integrations in that one 500 bp segment. For the "hotspot" with 280 times more integration events, that is about 900 integration events in the hotspot with 10 million insertions elsewhere in the genome. That means that just 0.009% of the insertions happen in the hotspot.
Since the lying creationists at the Discovery Institute are trying to argue that orthologous ERV's are due to target site preferences, then the percentage of orthologous ERV's to total ERV's should be 0.009%. Is that what we see? Not even close. The percentage of orthologous ERV's is 99.95% for the human genome.
Complete fail on the part of the Discovery Institute.
Do Shared ERVs Support Common Ancestry? - Evolution News & Views
They try to insinuate that retroviral locus-specific site preference can result in the pattern of ERV's shared by humans and chimps. Of course, they try to claim that just 12 out of "tens of thousands" are orthologous, so obviously their argument falls apart right away. However, it is worth the time to sweep up the other nonsense they have in their "article".
They cite a paper by Sverdlov paper that itself references this paper:
Distribution of targets for avian retrovirus DNA integration in vivo.
In the real scientific paper, the authors state that one of their integration sites saw a rate of integration 280 times higher than what would be expected from purely random insertion. So what does that really mean? From the paper:
"In all experiments, estimates of the m.o.i. ranged from two to three integrated proviruses per cell. A pool of 10 ug of infected TEF DNA (from -5x 10^6 cells) would therefore contain ~1-1.5 x 10^7 integration events. If integration occurred at random throughout the gehome (size 2x 10^9 bp) we would expect to see about two to three integrations, in each orientation, within the 500-bp stretch of DNA analyzed in each reaction."
So, out of 10 million integrations, they would expect 3 integrations in that one 500 bp segment. For the "hotspot" with 280 times more integration events, that is about 900 integration events in the hotspot with 10 million insertions elsewhere in the genome. That means that just 0.009% of the insertions happen in the hotspot.
Since the lying creationists at the Discovery Institute are trying to argue that orthologous ERV's are due to target site preferences, then the percentage of orthologous ERV's to total ERV's should be 0.009%. Is that what we see? Not even close. The percentage of orthologous ERV's is 99.95% for the human genome.
Complete fail on the part of the Discovery Institute.
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Since crazyforgod probably doesn't even understand the opening post or why the Discovery Institute article is a load of bovine excrement, I will continue on with my documentation of their complete failure.
One of the things that they actually get right is that there are a handful of exceptions to the expected nested hierarchy, sort of. From the DI article:
"We are (incorrectly) told that "There is only one, solitary known deviation of the distributional nested hierarchy; a relatively recently endogenized/fixed ERV called HERV-K-GC1." "
It is true that HERV-K-GC1 does not follow the expected pattern. However, a few outliers amongst 200,000 is to be expected with incomplete lineage sorting, and even possible independent insertions. The (incorrectly) part is where the DI really jumps the shark.
They try to pretend that PTERV1 insertions in different primate species are orthologous, and therefore violate the expected nested hierarchy. If they understood the part they quoted, they could have avoided the embarrasing contrafactual conclusion that they drew in the last sentence of the part I quoted above.
Is there a single unambiguous PTERV1 insertion that deviates from the orthodox phylogeny? Nope. Let's look at the Yohn (2005) paper. Their first screen used BAC clones which use large chunks of DNA. The resolution of the BAC clone method is limited by the size of DNA in the BAC clone. Here is what they found:
Therefore, 275 out of the 299 insertions were not even within 160,000 bases of each other. Definitely not orthologous, and definitely lineage specific and therefore not a deviation from the expected nested hierarchy. That leaves 24 that are within 160,000 base pairs of each other which is a pretty big area. So what happened when the tried to map it down to the single base level?
For the 3 shared by chimps and macaques, two were unambiguously not orthologous and the remaining one could not be resolved due to repeats. For the remainder, they didn't have the sequence data available.
IOW, they didn't find a single unambiguous example of a PTERV1 insertion that was found at an orthologous position between any primate species. This is ENTIRELY consistent with the orthodox phylogeny.
It is also a direct counterargument to both the "common building blocks" camp and the "independent insertion" camp. Not only can the theory of evolution predict which ERV's will be orthologous, it can also predict which ones will be non-orthologous. Here we have the exact same virus in numerous species, but none of them are found at the same genetic locus as the theory of evolution predicts.
Once again, massive failure on the part of the Discovery Institute that outright lies about the PTERV1 insertions found in primates.
One of the things that they actually get right is that there are a handful of exceptions to the expected nested hierarchy, sort of. From the DI article:
"We are (incorrectly) told that "There is only one, solitary known deviation of the distributional nested hierarchy; a relatively recently endogenized/fixed ERV called HERV-K-GC1." "
It is true that HERV-K-GC1 does not follow the expected pattern. However, a few outliers amongst 200,000 is to be expected with incomplete lineage sorting, and even possible independent insertions. The (incorrectly) part is where the DI really jumps the shark.
In addition to the case mentioned, Yohn et al. (2005) report:
"We performed two analyses to determine whether these 12 shared map intervals might indeed be orthologous. First, we examined the distribution of shared sites between species (Table S3). We found that the distribution is inconsistent with the generally accepted phylogeny of catarrhine primates. This is particularly relevant for the human/great ape lineage. For example, only one interval is shared by gorilla and chimpanzee; however, two intervals are shared by gorilla and baboon; while three intervals are apparently shared by macaque and chimpanzee. Our Southern analysis shows that human and orangutan completely lack PTERV1 sequence (see Figure 2A). If these sites were truly orthologous and, thus, ancestral in the human/ape ancestor, it would require that at least six of these sites were deleted in the human lineage. Moreover, the same exact six sites would also have had to have been deleted in the orangutan lineage if the generally accepted phylogeny is correct. Such a series of independent deletion events at the same precise locations in the genome is unlikely (Figure S3).
[...]
Several lines of evidence indicate that chimpanzee and gorilla PTERV1 copies arose from an exogenous source. First, there is virtually no overlap (less than 4%) between the location of insertions among chimpanzee, gorilla, macaque, and baboon, making it unlikely that endogenous copies existed in a common ancestor and then became subsequently deleted in the human lineage and orangutan lineage. Second, the PTERV1 phylogenetic tree is inconsistent with the generally accepted species tree for primates, suggesting a horizontal transmission as opposed to a vertical transmission from a common ape ancestor. An alternative explanation may be that the primate phylogeny is grossly incorrect, as has been proposed by a minority of anthropologists."
As irritating to the evolutionary model as it might be, there are, in fact, a significant number of deviations from the orthodox phylogeny.
"We performed two analyses to determine whether these 12 shared map intervals might indeed be orthologous. First, we examined the distribution of shared sites between species (Table S3). We found that the distribution is inconsistent with the generally accepted phylogeny of catarrhine primates. This is particularly relevant for the human/great ape lineage. For example, only one interval is shared by gorilla and chimpanzee; however, two intervals are shared by gorilla and baboon; while three intervals are apparently shared by macaque and chimpanzee. Our Southern analysis shows that human and orangutan completely lack PTERV1 sequence (see Figure 2A). If these sites were truly orthologous and, thus, ancestral in the human/ape ancestor, it would require that at least six of these sites were deleted in the human lineage. Moreover, the same exact six sites would also have had to have been deleted in the orangutan lineage if the generally accepted phylogeny is correct. Such a series of independent deletion events at the same precise locations in the genome is unlikely (Figure S3).
[...]
Several lines of evidence indicate that chimpanzee and gorilla PTERV1 copies arose from an exogenous source. First, there is virtually no overlap (less than 4%) between the location of insertions among chimpanzee, gorilla, macaque, and baboon, making it unlikely that endogenous copies existed in a common ancestor and then became subsequently deleted in the human lineage and orangutan lineage. Second, the PTERV1 phylogenetic tree is inconsistent with the generally accepted species tree for primates, suggesting a horizontal transmission as opposed to a vertical transmission from a common ape ancestor. An alternative explanation may be that the primate phylogeny is grossly incorrect, as has been proposed by a minority of anthropologists."
As irritating to the evolutionary model as it might be, there are, in fact, a significant number of deviations from the orthodox phylogeny.
They try to pretend that PTERV1 insertions in different primate species are orthologous, and therefore violate the expected nested hierarchy. If they understood the part they quoted, they could have avoided the embarrasing contrafactual conclusion that they drew in the last sentence of the part I quoted above.
Is there a single unambiguous PTERV1 insertion that deviates from the orthodox phylogeny? Nope. Let's look at the Yohn (2005) paper. Their first screen used BAC clones which use large chunks of DNA. The resolution of the BAC clone method is limited by the size of DNA in the BAC clone. Here is what they found:
We then compared the locations (Figure 3; Table 2) between species to determine whether the sites were non-orthologous. Based on an analysis of 1,467 large-insert clones, we mapped 299 retroviral insertion sites among the four species (Figure 3; Table S2). A total of 275 of the insertion sites mapped unambiguously to non-orthologous locations (Table 2), indicating that the vast majority of elements were lineage-specific (i.e., they emerged after the divergence of gorilla/chimpanzee and macaque/baboon from their common ancestor).
Within the limits of this BAC-based end-sequencing mapping approach, 24 sites mapped to similar regions of the human reference genome (approximately 160 kb) and could not be definitively resolved as orthologous or non-orthologous (Table S3).
Within the limits of this BAC-based end-sequencing mapping approach, 24 sites mapped to similar regions of the human reference genome (approximately 160 kb) and could not be definitively resolved as orthologous or non-orthologous (Table S3).
Therefore, 275 out of the 299 insertions were not even within 160,000 bases of each other. Definitely not orthologous, and definitely lineage specific and therefore not a deviation from the expected nested hierarchy. That leaves 24 that are within 160,000 base pairs of each other which is a pretty big area. So what happened when the tried to map it down to the single base level?
For the three intervals putatively shared between macaque and chimpanzee, we attempted to refine the precise position of the insertions by taking advantage of the available whole-genome shotgun sequences for these two genomes. For each of the three loci, we mapped the precise insertion site in the chimpanzee and then examined the corresponding site in macaque (National Center for Biotechnology Information). In one case, we were unable to refine the map interval owing to the presence of repetitive rich sequences within the interval. In two cases, we were able to refine the map location to single basepair resolution (Figures S4 and S5). Based on this analysis, we determined that the sites were not orthologous between chimpanzee and macaque. . . Although the status of the remaining overlapping sites is unknown, these data resolve four additional sites as independent insertion events and suggest that the remainder may similarly be non-orthologous.
For the 3 shared by chimps and macaques, two were unambiguously not orthologous and the remaining one could not be resolved due to repeats. For the remainder, they didn't have the sequence data available.
IOW, they didn't find a single unambiguous example of a PTERV1 insertion that was found at an orthologous position between any primate species. This is ENTIRELY consistent with the orthodox phylogeny.
It is also a direct counterargument to both the "common building blocks" camp and the "independent insertion" camp. Not only can the theory of evolution predict which ERV's will be orthologous, it can also predict which ones will be non-orthologous. Here we have the exact same virus in numerous species, but none of them are found at the same genetic locus as the theory of evolution predicts.
Once again, massive failure on the part of the Discovery Institute that outright lies about the PTERV1 insertions found in primates.
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Just so we can keep score, the DI lied about:
1. The number of orthologous ERV's shared by humans and chimps.
2. The ability of locus-specific site preference to produce the number of orthologous ERV's shared by humans and chimps.
3. PTERV1 insertions deviate from the orthodox phylogeny.
I actually went through 3 of their lies. I could probably find a few more minor ones, but those are the biggies.
1. The number of orthologous ERV's shared by humans and chimps.
2. The ability of locus-specific site preference to produce the number of orthologous ERV's shared by humans and chimps.
3. PTERV1 insertions deviate from the orthodox phylogeny.
I actually went through 3 of their lies. I could probably find a few more minor ones, but those are the biggies.
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justlookinla
Regular Member
'yer a liar' over and over and over and over and over.
I'm not sure why you even bother to use different alters.
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Did you read the posts where I exposed their lies?
Also, I am not the one who brought those lies into the conversation. Someone else referenced the lying creationist site, so I showed them all of the lies.
If you don't want me to point out lies, then don't post lies. Simple.
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You are probably wasting your time. I remember well my struggles with him trying to get him to admit that weather and volcanoes were not random. I finally dropped it because I saw that nothing was going to get through.
I don't think he has responded yet to any of the evidence in this thread just used his standard responses for evidence avoidance.
Just has a few simple set responses to any evidence presented to him.
1. Deny it is evidence
2. Change the subject
3. Go to the "only" mantra
4. Name calling (This is fairly new but he appears to be using it a lot lately.)
What he does not do is look at the evidence and I honestly don't think anything can get him to.
Dizredux
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Resha Caner
Expert Fool
I don't want to interrupt the lecture, but I do have a few questions about ERVs when the time is right.
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justlookinla
Regular Member
This is why folks shouldn't claim that only naturalistic mechanisms produced humanity from a single life form of long long ago. Your ERV viewpoint is nothing more than your viewpoint, tainted by Godless evolutionism.
1Jn 2:22 Who is a liar but he that denieth that Jesus is the Christ? He is antichrist, that denieth the Father and the Son.
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justlookinla
Regular Member
When the conversation began turning to the implications of weather and volcanoes....and earthquakes.....not being random, folks started dropping out quickly.
There is no evidence for evolutionism.
The question of what/who produced humanity hasn't been answered by any evidence.
Using scripture to identify those who reject Christ isn't name calling.
1Jn_2:18 Little children, it is the last time: and as ye have heard that antichrist shall come, even now are there many antichrists; whereby we know that it is the last time.
1Jn_2:22 Who is a liar but he that denieth that Jesus is the Christ? He is antichrist, that denieth the Father and the Son.
1Jn_4:3 And every spirit that confesseth not that Jesus Christ is come in the flesh is not of God: and this is that spirit of antichrist, whereof ye have heard that it should come; and even now already is it in the world.
2Jn_1:7 For many deceivers are entered into the world, who confess not that Jesus Christ is come in the flesh. This is a deceiver and an antichrist.
1Jn_2:22 Who is a liar but he that denieth that Jesus is the Christ? He is antichrist, that denieth the Father and the Son.
1Jn_4:3 And every spirit that confesseth not that Jesus Christ is come in the flesh is not of God: and this is that spirit of antichrist, whereof ye have heard that it should come; and even now already is it in the world.
2Jn_1:7 For many deceivers are entered into the world, who confess not that Jesus Christ is come in the flesh. This is a deceiver and an antichrist.
Are you having problem with scripture?
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I do have a problem with evident glee you seem to get from throwing that term around to get out of discussing the evidence.
You will not look at web sites and will not use books or journals to check out evidence presented to you.
You constantly insist that someone put the evidence on the forum where you do not have to work to see it. Loudmouth went to a good bit of effort to comply with your wishes and posted the evidence a separate thread so you could respond and you refuse to address the evidence he presented.
Rather hypocritical don't you think?
Go on Just, discuss the evidence.
Dizredux
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Weak.
Posts #102 and #103 are brimming over with evidence.
Would you care to address the evidence?
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OK then analyze the evidence presented and explain why you do not consider it to be adequate. Be specific as you can.
Dizredux
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Doveaman
Re-Created, Not Evolved.
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It is also evidence for Human Re-Creation.
And God made prehistoric man from the decomposed remains (dust) of prehistoric ape.
And God made modern man from the decomposed remains (dust) of prehistoric man.
Prehistoric ape --> Prehistoric man --> Modern man (Adam).
It's not complicated.
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A
Andy 998
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I'm with you because I love magic as well, I love trying to work out how they do it.
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As you have been asked *many* times, can you show where this being said in any science format? In other words who is claiming this?
Isn't it somewhat dishonest to keep making statements like this but never attempting to back them up when asked?
Dizredux
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