Chimpanzee Genome

[WisdomTree]

I don't get the poll...

 

[mark kennedy]

The only reason you know what the indel numbers are is because they reported them and discussed them. Why do we need to avoid the indels? Please explain.

Because you can't explain how mutations that size could happen without creating an extinction event. If you can't explain it, then just ignore it, like the human brain. Louise Leaky couldn't find hominid skulls so he just ignored the cerebral rubicon. That way he could take ape skulls and pass them off as our ancestors. That's why there are no chimpanzee skulls in natural history museums, they mark them HomoXXX in a desperate ploy to fabricate the mythical transitional.

Empty assertions. You need evidence to back this up.

You got your nerve, you haven't been able to substantiate your facts once.

 

[mark kennedy]

I don't get the poll...

Mutations most often do nothing, thus they are neutral, mostly because they are not a part of genes that do stuff. When they do have an effect they are either harmful or beneficial. You can have beneficial effects in rare instances but they simple don't happen in brain related genes.

Polls in these threads are usually just for my own personal amusement. I like to have them to see who is lurking in the shadows.

 

[Loudmouth]

The indels are simply gaps, differences of length. Of course they are counted unless they don't fit one of these homology arguments, then they are ignored.

Right, because evolution does not predict species specific sequences that produce divergence . . . oh wait, it does.

I guess you are unaware the evolution is CHANGE over time? What do you think is changing? Could it be DNA sequence?

So why are you pointing to divergence as evidence against evolution when divergence IS THE VERY THING IT PREDICTS?

Right, but they are not 1% of the human genome they are 8%.

Then why do you keep citing the 1% number if you know that it is wrong?

Did they grow in length over the five years it took for the revision to finally emerge?

They sequenced more of the genome and found more ERV's than they had before.

Of course you need a Chimpanzee Genome to compare them to otherwise you are making a false assumption that they are actually the same.

But we don't need a chimp genome to know how many are in the human genome, and that number is 200,00. When the chimp genome was sequenced then we did know how many were the same, and that number is 99.99% of those 200,000.

[quoite]The PERVs are the most abundant family of ERVs . . .[/quote]

Of the 425 ERV's they looked at. You keep forgetting to mention that. They looked at 0.02% of the ERV's in the chimp genome.

and make up 7% of the divergence.

Yes, 7% of the 35 million bases of chimp specific sequence for a grand total of 2.45 million bases. At ~300 chimp specific ERV's that's about 8kb per ERV which is right in the ballpark:

"The average size of full-length class I CERVs is 8,443 bp. These elements range in size from 2,268 to 13,135 bp in length."
Identification, characterization and comparative genomics of chimpanzee endogenous retroviruses

So where is the problem again?

That is a fact you are not running away from but obviously unaware of. Your not making an actual comparison, your just throwing numbers out there and pretending they are accurate.

Another irony meter explodes. Looks like I had better buy in bulk for this thread.

So far you haven't manage to substantiate any of them.

Let's start with the number of ERV's in the human genome which is ~200,000 according to Table 11 from the human genome paper:

Table 11 : Initial sequencing and analysis of the human genome : Nature

Please tell me how I have not substantiated this fact.

I've seen how you 'extrapolate' and it's bogus. So far you have failed to substantiate that claim, or even attempt to.

Table 11, human genome paper. Look at it. 200,000 human ERV's are substantiated. Look at the chimp genome paper. Less that 100 human ERV's are specific to humans MEANING THE REST ARE SHARED WITH CHIMPS.

Facts substantiated.

The Polavarapu et. al (2006) paper only looked at 425 ERV's. Substantiated. You extrapolating from 0.02% of all ERV's to the rest? Yep, that is EXACTLY what you are doing.

Because it's not true.

With more than 100 members, CERV 1/PTERV1 is one of the most abundant families of endogenous retroviruses in the chimpanzee genome. (Genome Biol. 2006).​

​

Of the 425 ERV's they looked at which is just 0.02% of the ERV's in the chimp genome.

You have never managed to answer that point.

It doesn't matter, your trailing off on irrelevant details

The pattern of orthology amongst ERV's found in humans and apes is the most relevant of details. That is what makes ERV's evidence. ERV's produce an unmistakeable phylogenetic signal, one that evolution predicts should be there, and it is there. Creationism can not explain this signal.

Orthologous simple means the same.

It means much more than that. For ERV's, the location of the insertion in the genome determines if it is orthologous or not. Different insertions will still have homologous genes, but they will not be orthologous. Evolution predicts that given the species distrubution of the PtERV1 insertions that they occurred after the split between humans and chimps. Therefore, PtERV1 insertions between chimps and gorillas should not be found at the same genome location because they are independent events. Guess what? That prediction is borne out. The PtERV1 insertions in the gorilla and chimp genomes do not occur at the same base in each genome. They occur at different locations just as the theory of evolution predicts.

So please tell me why testable and accurate predictions made by the theory of evolution with respect to ERV's are not relevant to this discussion?

No, you have a dated list that shows ERVs are 1% of the human genome, they percentage has jumped up to 8%. Don't think your source material is reliable.

So now you are ignoring the human genome paper? How convenient for you. What next? ERV's don't exist?

At least 7% of the divergence between us and Chimpanzees is due to these ERVs and you would have me believe that they are virtually all identical. It's absurd.

More salesmanship on percentages from Mark. We are talking about 7% of the 1.5% divergence for an overall divergence of 0.105% divergence due to ERV's, and the math also adds up as I demonstrated above.

Don't need a molecular clock, need a mutation rate.

The mutation rate is determined by the divergence of neutral sequence, not sequence that is under selection. That is genetics 101.

 

[Loudmouth]

Because you can't explain how mutations that size could happen without creating an extinction event.

Do humans have those indels? Yes. Are we extinct? No.

Problem explained.

If you can't explain it, then just ignore it, like the human brain.

If I showed you a pygmy brain with a size of 1200 ccm and a large European brain with a size of 2000 ccm that was 20 years older would you conclude that the human brain size nearly doubled in 20 years?

Louise Leaky couldn't find hominid skulls so he just ignored the cerebral rubicon. That way he could take ape skulls and pass them off as our ancestors. That's why there are no chimpanzee skulls in natural history museums, they mark them HomoXXX in a desperate ploy to fabricate the mythical transitional.

So what features would a real transitional have?

You got your nerve, you haven't been able to substantiate your facts once.

Table 11, human genome paper.

 

[Notedstrangeperson]

No it hasn't, I stopped posting here because they didn't want to admit that the claim that we are 98% the same in our DNA is wrong. If you think this point has been refuted suppose you tell me, are we 98% the same as Chimpanzees in our DNA or not? The ERVs are not really proof of anything but they are not identical in the two genomes, in fact, the single most abundant family of ERVs is absent in the human genome. Neither of these points have been refuted because they can't be.

Yeah, they have been refuted. Whether humans are 98% genetically identical to chimps depends on what part of the genome you're measuring. And as far as I know retroviruses are not necessarily an indicator of ancestry because they are capable of infecting most living organisms. Cows and other ruminants (but not other mammals) and snakes share a retrovirus, but I doubt that means cows are more closely related to snakes than they are to, say, horses.

Yea that's the famous trick of Darwinism, when you can't explain it just move the date back. There's one major problem with that, we don't have any chimpanzee ancestors in the fossil record for 25 million years. The ERVs, BTW, for the most part go back about 25 million years ago. I really don't know what moving the date back does for you but it looks like the only way to explain the divergence to me.

We don't have many chimps fossils at all, unfortunately. But I highly doubt we would find any as old as 25 million, simply because they did not exist that long ago. As far as I am aware no apes existed that long ago. They would only just have diverged from monkeys.

 

[Loudmouth]

Yeah, they have been refuted. Whether humans are 98% genetically identical to chimps depends on what part of the genome you're measuring. And as far as I know retroviruses are not necessarily an indicator of ancestry because they are capable of infecting most living organisms. Cows and snakes share a retrovirus.

Retroviruses insert randomly amongst millions of possible insertion sites in the host genome. Finding the same insertion at the same position in two species genome is an indication that the insertion happened in a common ancestor since two independent insertions would occur at two different sites in the genome.

 

[Notedstrangeperson]

Retroviruses insert randomly amongst millions of possible insertion sites in the host genome. Finding the same insertion at the same position in two species genome is an indication that the insertion happened in a common ancestor since two independent insertions would occur at two different sites in the genome.

I changed my post while you were replying to it. I added " Cows and other ruminants (but not other mammals) and snakes share a retrovirus, but I doubt that means cows are more closely related to snakes than they are to, say, horses."

I know some retroviruses can be inherited, but in some cases - such as the cow and the snake - they don't seem to be an indicator of common ancestry.

I'm not sure whether the paper Mark Kennedy was referring to argued that ERVs shared by humans and chimps was an indicator of common ancestry or not.

 

[Tomk80]

I changed my post while you were replying to it. I added " Cows and other ruminants (but not other mammals) and snakes share a retrovirus, but I doubt that means cows are more closely related to snakes than they are to, say, horses."

I know some retroviruses can be inherited, but in some cases - such as the cow and the snake - they don't seem to be an indicator of common ancestry.

I'm not sure whether the paper Mark Kennedy was referring to argued that ERVs shared by humans and chimps was an indicator of common ancestry or not.

It did. The reason why it did, is that in these cases the ERV is orthologous. The ERV occurs in the same place of the genome for both chimps and humans. The argument is not based solely on the sequence of the ERV.

IIRC, the ERV for ruminants and snakes you mentioned is not orthologous. In other words, same ERV, different spot in the genome. But I'd need to see a reference for that to check it.

 

[Loudmouth]

I changed my post while you were replying to it. I added " Cows and other ruminants (but not other mammals) and snakes share a retrovirus, but I doubt that means cows are more closely related to snakes than they are to, say, horses."

I know some retroviruses can be inherited, but in some cases - such as the cow and the snake - they don't seem to be an indicator of common ancestry.

All ERV's are inherited. What is important is where in the genome the ERV's are found. With distantly related organisms such as snakes and cows I really doubt you could detect synteny and orthology anyway, so the point is a bit moot anyway. However, with chimps and apes the genomes are still very, very similar and "in order" for the vast majority of the genome. This allows us to determine if a retroviral insertion occurred at the same base in both genomes, that is whether or not the insertion is orthologous.

I'm not sure whether the paper Mark Kennedy was referring to argued that ERVs shared by humans and chimps was an indicator of common ancestry or not.

They were able to determine that PtERV1 were responsible for divergence between chimps and humans because they were not found in the human genome. However, hundreds of thousands of ERV's are found at the same location in both the chimp and human genomes which is smoking gun evidence of common ancestry. It's like finding two books that are only different in one word out of every 10,000.

 

[MrsLurking]

The mutation rate is determined by the divergence of neutral sequence, not sequence that is under selection. That is genetics 101.

Enduring Mark Kennedy's diatribes is like watching a an elementary genetics class where a D student who lacked the course prerequisites is a full-time heckler whining from the back of the room---because he thinks he knows how to correct the professor and tutor the Royal Academy of Science. Spare us! It is like fingernails on a chalkboard.

 

[Notedstrangeperson]

It did. The reason why it did, is that in these cases the ERV is orthologous. The ERV occurs in the same place of the genome for both chimps and humans. The argument is not based solely on the sequence of the ERV.

In which case I guess my particular criticism was wrong.

 

[Loudmouth]

Just so Mark can not wiggle out of this, here is Table 11 from the human genome paper. Notice the units are (x 1,000) for the number of copies at the head of the table.

 

[Loudmouth]

In which case I guess my particular criticism was wrong.

This analogy might help.

Imagine two people with two identical unabridged Oxford dictionaries. You ask them to randomly thumb through and plant their finger on 100 words and record which words they randomly ended up on. You then compare the lists. What are the chances that 99 out of 100 of the words are the same between the two people?

This is what ERV's are like. The retrovirus randomly inserts into one of millions of possible sites. The chances of 99 out of 100 insertions insertions occurring at the same base between two species is really, really low. In the case of humans and chimps, we only have 200 or so different "words" out of 200,000. The chances of this occurring due to independent events is just absurd. The only explanation is that these insertions occurred once in a common ancestor.

 

[Notedstrangeperson]

Loudmouth: Thanks for the explanation.

 

[MrsLurking]

Loudmouth: Thanks for the explanation.

Evidence is a wonderful thing.

(Will Mark Kennedy or AV1611vet listen to the evidence which God has provided in his creation? No.)

 

[mark kennedy]

Enduring Mark Kennedy's diatribes is like watching a an elementary genetics class where a D student who lacked the course prerequisites is a full-time heckler whining from the back of the room---because he thinks he knows how to correct the professor and tutor the Royal Academy of Science. Spare us! It is like fingernails on a chalkboard.

There is always a troll like you in these debates, it's the only thing that is truly consistent in these forums. Your job is to do nothing but insult me and any Creationist that posts to these forums, that is all you know how to do.

It's not only a fallacious approach to the subject but it's also a flagrant rules violation. I don't report it in here because for me it's one of the most important proofs that the few scientists who post here lack the convictions of their believes. If they really believed what they were saying they would simply defend their views and be done with it. Since they can't they encourage you and those like you to be nasty with Creationists, convincing you that your much smarter then they are because of it.

You can let yourself be used in this way, it does nothing but encourage me. I just think it's sad that such an amazing thing like the development and advancement of genetics over the last century will never be of interest to you. You have managed to abandon scientific thought completely, you have not so much as mentioned genomics or any of the many particulars involved in comparative genomics.

Your only purpose in these debates is to be nasty, bitter and offensive. It's called flaming and the fact that the actual evolutionists on here encourage you speaks volumes for their lack of confidence in their own philosophy.

 

[MrsLurking]

There is always a troll like you in these debates, it's the only thing that is truly consistent in these forums. Your job is to do nothing but insult me and any Creationist that posts to these forums, that is all you know how to do.

It's not only a fallacious approach to the subject but it's also a flagrant rules violation. I don't report it in here because for me it's one of the most important proofs that the few scientists who post here lack the convictions of their believes. If they really believed what they were saying they would simply defend their views and be done with it. Since they can't they encourage you and those like you to be nasty with Creationists, convincing you that your much smarter then they are because of it.

You can let yourself be used in this way, it does nothing but encourage me. I just think it's sad that such an amazing thing like the development and advancement of genetics over the last century will never be of interest to you. You have managed to abandon scientific thought completely, you have not so much as mentioned genomics or any of the many particulars involved in comparative genomics.

Your only purpose in these debates is to be nasty, bitter and offensive. It's called flaming and the fact that the actual evolutionists on here encourage you speaks volumes for their lack of confidence in their own philosophy.

Incredible. Denial of the evidence is not discourse. And hypocrisy does not go unnoticed. Play the martyr even while you fit your blinders, wear your ear-plugs, and heckle the scientists. Nobody is fooled.

Here's a brief trolling review:

1) "Yea that's the famous trick of Darwinism, when you can't explain it just move the date back."

2) "That's why there are no chimpanzee skulls in natural history museums, they mark them HomoXXX in a desperate ploy to fabricate the mythical transitional."

3) ""For reasons I can't quite grasp no evolutionist will touch the mutation rate with a ten foot pole."

Lie much?

Troll, troll, troll your boat......

 

[mark kennedy]

Just so Mark can not wiggle out of this, here is Table 11 from the human genome paper.

Wiggle out? Dude, you doing what you always do, painting yourself into a corner. What the table says is that the ERV class 1 sequences are 79 million base pairs total, comprising under 3% of the entire sequence with 72 families. Ok, this is what we know about the Chimpanzee Genome:

According to this table the Chimpanzee Genome has 234 ERV class 1 elements greater the 1 million base pairs (MPS). Do you see a problem here yet?

 

[mark kennedy]

Incredible. Denial of the evidence is not discourse. And hypocrisy does not go unnoticed. Play the martyr even while you fit your blinders, wear your ear-plugs, and heckle the scientists. Nobody is fooled.

Only one actual scientist posted in this thread, Steve and he wasn't interested in the discussion. I am neither offended nor threatened by your theatrics, I'm informed by them. Why would a scientist need you?

Here's a brief trolling review:

1) "Yea that's the famous trick of Darwinism, when you can't explain it just move the date back."

That was one point I made but that's gradualism for you, they literally have all the time in the world.

2) "That's why there are no chimpanzee skulls in natural history museums, they mark them HomoXXX in a desperate ploy to fabricate the mythical transitional."

Ok, so where are the Chimpanzee ancestors in the fossil record then? Go ahead and google it and what you will find is that they have found three maybe four teeth. If they were not alive today there would be no evidence that they ever existed, you can't say that about the gorillas. Bet you don't know why you can't use a gorilla skull as a hominid ancestor?

Lie much?

Everything I have said is either inescapably true or a matter of opinion. Especially true is the fact that there is always a troll in these threads. They are unmistakable, they have absolutely no interest in or knowledge of scientific facts or evidence. They never make a single substantive statement. They are here for one thing and one thing only, to be as nasty to Creationists as possible.

It's called the ad hominem fallacy and you are demonstrating the most important proof a Creationist would ever need to see the failure of Darwinism. They always have to resort to this kind of fallacious logic or they will have to answer based on the actual evidence. The fact that they need you tells me in no uncertain terms that they don't have the courage of their convictions.