Similarity of human and chimp DNA is down.

[cupid dave]

Those two sequences are completely arbitrary. I just made them up. We are talking about the method used to compare sequences. Do you think it is correct to say that those two sequences are 96.67% identical or 0% identical?

Well there are say 29 AAAAA's in each and then one ends differently with T.

So, the % similarity is 29/30X100% = 96.67%.

But we all know that humans have 23 Chromosome pairs while chimps have 24.

Right?

 

[Zaius137]

So what ended up in the bucket? I apologize for the lack of patients but I really see the end of the line for this posting.

This is what you said back then…

"Only 2.7 Gb of chimpanzee genome was even sequenced successfully, so the maximum that could have been aligned would have been those 2.7 Gb, even if the genomes were identical."

Were they identical… if you do not know why mention it?

"The first supplementary note (linked above) describes what happened to the remaining 0.3 Gb that didn't align. 0.24 Gb could be aligned, but the alignments were to many places in the human genome, so the sequence was discarded."

So .3Gb hit the bit bucket. Leaving 2.4Gb.

This is what you say now…

"An additional 0.09 Gb of chimpanzee sequence did not align at all to human."

.09/3.1~3% of total genome did not align from these fragments.

"These together total a little over 2.7 Gb, which is the amount of chimpanzee genome that was sequenced."

But the .3Gb did get sequenced and discarded?

I appreciate the detail, I really do, but what is the bottom line?

I think you know what I am going to do with the figure you give me. I can’t blame some scientists that inflate the numbers just for effect but there is a time to put the cards on the table, so here is the call.

So are we at 2.4Gb or 2.7Gb? I will go with your figure between these two values.

 

[USincognito]

But we all know that humans have 23 Chromosome pairs while chimps have 24.

Right?

Yep, and some of us know why that is the case. A chromosome fusion occured after the chimp/hominan LCA producing human chromosome 2.
Chromosome 2 (human) - Wikipedia, the free encyclopedia

 

[USincognito]

The AVERAGE similarity across those two 10 bp sequences is 90% because 9 out of 10 bases match. If I were doing a 10 bp comparison instead of a 1 bp comparison the similarity would be 0%. Do you understand this or not? Why is this so hard to understand?

We all understand the mathmatical sleight of hand that Creationists engage in. We all understand how blatanly transparent such chicanery is as well. I think we all also understand the problem is with you, not with us.

 

[sfs]

?
read more:


The Last Human: A Guide to Twenty-Two Species of Extinct Humans
by G.J. Sawyer, Viktor Deak
Hardcover, 256 pages
Published June 28th 2007 by Yale University Press

Did you read what you were responding to? The 22 species in question represent one rather arbitrary way of dividing up the fossils since our most recent common ancestor with chimpanzee. There are vast numbers of earlier fossil species that would qualify as well.

Compare these 22 extinct species to the 22 names from Adam through Noah's three sons, Caucasian, Negroid, and mongoloid.


see this link:
Gen 5:25-32

Okay, having compared them I see nothing at all in common between them. So what's the point?

 

[cupid dave]

Yep, and some of us know why that is the case. A chromosome fusion occured after the chimp/hominan LCA producing human chromosome 2.
Chromosome 2 (human) - Wikipedia, the free encyclopedia

Yes, and that was a beneficial mutation, right?

But jow many people ever realozed that drom that point on, 22 more species would follow just like it says in Genesis 5?

 

[USincognito]

Yes, and that was a beneficial mutation, right?

No, it was a chromosomal fusion. The genes within the chromosomes themselves didn't change.

But jow many people ever realozed that drom that point on, 22 more species would follow just like it says in Genesis 5?

Probably very, very few. And there's a good reason for that.

 

[Zaius137]

"No, it was a chromosomal fusion. The genes within the chromosomes themselves didn't change."

I can't let this one go by... what do you mean they did not change? What about the imiediate areas around the centromeres and telomeres?

 

[Zaius137]

My conclusion statement is in the following dialog.

“To be termed scientific, a method of inquiry must be based on gathering empirical and measurable evidence subject to specific principles of reasoning.”

http://en.wikipedia.org/wiki/Scientific_method

My understanding is “principles of reasoning” excludes biased presuppositions.

What are the empirical findings?

1. In the published chimp genome only 2.4Gb was included in the sequencing of the chimp genome.
2. The human genome is ~3.1Gb long.
3. This gives 2.4Gb/3.1Gb that was compared, therefore limiting the conclusion at this time to ~77% similarity as a maximum. In other words the findings are empirically limited to the evaluated genome amount.
4. The Chimp Genome divergence from the aligned portion of the genome yielded findings of ~1.4% divergent from the human genome. See note 1
5. The Uncommon Decent statistical evaluation of the human/chimp genomes found that they match only ~62% of the time. (.7Gb was excluded from the published genomes)
6. Using the poisson distribution and the ~1.4% divergence found in point (4). P(0)=e^-m, m=(1-.014), P(x)=(1-ans). P(x) ~63%. The probability of finding a match between the chimp/human genome segments is ~63% according to a ~1.4% difference.
7. The Uncommon Decent findings closely resemble the Chimp Genome project in comparable genomes. 62%~63%. Implying that the statistical method used by Uncommon Decent has some validity in similar findings.


Note 1: I think I need to point out that the published chimp genome is an artifact of alignment tools. Insertions and deletions of bp’s to even gene lengths and the correcting of indels only produces an artificial alignment to the human scaffold.


What conclusions did I come to?

1. At best the findings of the Chimp Genome project can only claim to be ~76% similar. From empirical findings 1,2,3,4.
2. Drawing a conclusion that the genomes are 98.6% the same is intellectually dishonest because of the missing .7Gb sequences from the data.
3. Also 98.6% only shows that the real genes line up 63% of the time. If taken in light of a null-hypothesis of being a statistical similarity the statement of 98.6% similarity conveys a predisposed conclusion of common decent. If you say that the two genomes only compare 63% of the time someone may view things differently.
4. No distinction between Common decent and common design can be made from the empirical evidence no matter what percentage of resemblance is found in the DNA.
5. As to (note 1) there is a basic presupposition implied by messaging the DNA of the chimp genome to align with the human scaffold. I find it possible to believe that associations in genes are erroneously being created by that messaging.

What I believe:

Given the evaluations by the chimp genome project and the Uncommon Decent article I am inclined to believe that evolutionary bias tends to push up the comparison numbers.

I will have to go with values of similarity no greater than 2.4Gb/3.1Gb ~76% leaning toward the original Wiki of possibly 70% similarity as the low (because the extraordinary measures taken in the alignment). I do not accept the 98.6% similarity as it misleads the uninformed public.

Order is all important and random insertions or deletions alter the coding frame of reference. I have a degree in programming and I can not imagine how to make a meaniful procedure code from multiple entry points forward and reverse. As far as I know it has never been done except by DNA.

As I mentioned before “Try ignoring 23% of the book “Huckleberry Finn” and see if you get the same reading.” I am truly surprised that some participants in this forum are willing to just disregard 23% of the chimp genome and assume it is just a technicality defying the efforts of the alignment tools.

 

[Loudmouth]

What are the empirical findings?

1. In the published chimp genome only 2.4Gb was included in the sequencing of the chimp genome.
2. The human genome is ~3.1Gb long.
3. This gives 2.4Gb/3.1Gb that was compared, therefore limiting the conclusion at this time to ~77% similarity as a maximum. In other words the findings are empirically limited to the evaluated genome amount.

77% would be the minimum. This figure assumes that none of the unaligned sequence would be similar to human DNA. If we go back to the early days of DNA sequencing when only a few genes were comparable between the two species then the figure would have been 0.0001% similarity using your same reasoning.

4. The Chimp Genome divergence from the aligned portion of the genome yielded findings of ~1.4% divergent from the human genome.

This is for base substitutions only. This figure does not include indels.

5. The Uncommon Decent statistical evaluation of the human/chimp genomes found that they match only ~62% of the time. (.7Gb was excluded from the published genomes)

You forgot to mention that random 30 bp segments match about 62% of the time. It is important to include the units that you are using. This figure is equivalent to the 1.4% difference when comparing base to base instead of 30 bp segments.

7. The Uncommon Decent findings closely resemble the Chimp Genome project in comparable genomes. 62%~63%. Implying that the statistical method used by Uncommon Decent has some validity in similar findings.

The original 1.4% was as statistical as the UD method. This 1.4% is a statistical mean of the probability that a base will match the same base in the other genome.

Note 1: I think I need to point out that the published chimp genome is an artifact of alignment tools.

So was the human genome that was reported in 2000. So are all genomes produced by whole genome shotgun methodologies. BAC clones combined with chromosome walking can produce much higher quality sequence, but it is much slower than the shotgun approach.

Insertions and deletions of bp’s to even gene lengths and the correcting of indels only produces an artificial alignment to the human scaffold.

This was not done. No bases were added to the reported chimp sequence so that they would produce the same genes as seen in humans. Again, you are confusing bases with alignment gaps.


What conclusions did I come to?

1. At best the findings of the Chimp Genome project can only claim to be ~76% similar.

The figure is ~98% of the sequence that they compared which comprises about 75% of the genome. The ~76% similarity is the MINIMUM similarity between the genomes, assuming that the ambiguously aligned sequence is 0% similar. Of course, this was not the case since the unaligned sequences had similarity to multiple portions of the human genome which is why these contigs were thrown out.

2. Drawing a conclusion that the genomes are 98.6% the same is intellectually dishonest because of the missing .7Gb sequences from the data.

It is not intellectually dishonest to say that there was 98.6% similarity between the DNA that was compared. Also, it is intellectually dishonest to claim that the rest of the genomes had no similarity which is what you are doing.

3. Also 98.6% only shows that the real genes line up 63% of the time.

Please define "line up". Also, non-coding DNA was compared in the UD method as well, not just genes.

If taken in light of a null-hypothesis of being a statistical similarity the statement of 98.6% similarity conveys a predisposed conclusion of common decent. If you say that the two genomes only compare 63% of the time someone may view things differently.

What only compares 63% of the time? Please show your units.

4. No distinction between Common decent and common design can be made from the empirical evidence no matter what percentage of resemblance is found in the DNA.

Of course not. Common design is unfalsifiable. There is no potential evidence that would convince you that common design was not involved. However, common ancestry is testable through such comparisons as orthologous ERV's.

5. As to (note 1) there is a basic presupposition implied by messaging the DNA of the chimp genome to align with the human scaffold. I find it possible to believe that associations in genes are erroneously being created by that messaging.

Belief has nothing to do with it. Either demonstrate it or withdraw the assertion.

Given the evaluations by the chimp genome project and the Uncommon Decent article I am inclined to believe that evolutionary bias tends to push up the comparison numbers.

The UD article and the chimp genome article produced the same results.

 

[Loudmouth]

Were they identical… if you do not know why mention it?

You completely missed the point. You could have two labs sequence 100% identical genomes and they would still have to throw out sections of the data because of poor alignment (especially in repeat regions).

I think you know what I am going to do with the figure you give me. I can’t blame some scientists that inflate the numbers just for effect but there is a time to put the cards on the table, so here is the call.

If you are against bloated numbers then why do you keep citing the UD study which purposefully bloats the numbers?

 

[Loudmouth]

Well there are say 29 AAAAA's in each and then one ends differently with T.

So, the % similarity is 29/30X100% = 96.67%.

According to the author over at Uncommon Descent the similarity between the two sequences is 0% because the sequence is not identical across the entire 30 base pairs. Is there any wonder why the reported value at UD is lower than the actual percent similarity?

But we all know that humans have 23 Chromosome pairs while chimps have 24.

And we also know that not all of those chromosomes are the same size.

 

[Loudmouth]

Let's have a scientist himself comment on the similarity of chimps and humans. Specifically the similarity of the recently-sequenced Y chromosome. Here's the link: Chimp Y chromosome

Let's have him submit the paper to a peer reviewed journal first.

 

[Naraoia]

?
read more:


The Last Human: A Guide to Twenty-Two Species of Extinct Humans
by G.J. Sawyer, Viktor Deak
Hardcover, 256 pages
Published June 28th 2007 by Yale University Press

I'm sorry, I'm not going to read 200+ pages for a forum argument. Please address my points in your own words.

OTOH Deak's art is really good. That book might actually be worth a look just for the pictures

Compare these 22 extinct species to the 22 names from Adam through Noah's three sons, Caucasian, Negroid, and mongoloid.

Can you please, please explain to me what special resemblance any Biblical figure bears to, I don't know, Paranthropus robustus?

(And can you please explain which of your three races Aborigines and San belong to?)

see this link:
Gen 5:25-32

I've seen more than enough of that link. You might as well stop plugging it.

Yes, and that was a beneficial mutation, right?

From what I know, it was probably neutral at best.

But jow many people ever realozed that drom that point on, 22 more species would follow just like it says in Genesis 5?

22 people are now 22 species?

"No, it was a chromosomal fusion. The genes within the chromosomes themselves didn't change."

I can't let this one go by... what do you mean they did not change? What about the imiediate areas around the centromeres and telomeres?

IIRC there aren't many genes in those areas. Sfs can confirm or correct me

 

[sfs]

IIRC there aren't many genes in those areas. Sfs can confirm or correct me

There are few, but not necessarily zero, genes in centromeres, but the centromeres were still there after the fusion, so they don't matter much one way or the other. There are no genes that I know of in telomerers. Telomeres are pieces of repetitive sequence that are routinely lost in replication and then replaced enzymatically, so they're really not a good place to find genes.

 

[LittleLambofJesus]

Similarity of human and chimp DNA is down.

This is the formal debate section. I suggest you report your own OP and request the mods move it to the main Creation and Evolution section.

That said, this was posted recently in the Origins Theology section by a geneticist who posts here......<snip>

Just subscribing for now

 

[Naraoia]

There are few, but necessarily zero, genes in centromeres, but the centromeres were still there after the fusion, so they don't matter much one way or the other. There are no genes that I know of in telomerers. Telomeres are pieces of repetitive sequence that are routinely lost in replication and then replaced enzymatically, so they're really not a good place to find genes.

Zaius was asking about the neighbourhood of *meres. Then again, given that the *meres themselves are still there, I don't imagine the "imiediate [sic] areas around" them were affected by the fusion.

 

[sfs]

Zaius was asking about the neighbourhood of *meres. Then again, given that the *meres themselves are still there, I don't imagine the "imiediate [sic] areas around" them were affected by the fusion.

Regulation of genes in the neighborhood of a fusion can be affected, I believe, which makes it hard to predict exactly what effect a fusion will have in practice. There are enough species around with varying chromosome counts to show that it is not always significantly deleterious.

 

[Zaius137]

Yes gene fusion is common and always (as far as I know) leads to reproductive problems as in the Robersonian fusion&#8230;

&#8220;Robertsonian rearrangements. A Robertsonian heterozygote is a cell which contains one metacentric chromosome which is homologous to two acrocentric chromosomes. If only one such Robertsonian fusion has occurred in a cell line, three chromosomes line up together during meiosis, rather than a bivalent. If the chromosomes separate properly during cell division, such heterozygotes may be fertile. If the chromosomes do not separate properly, the individual will be at least partially sterile. In a heterozygote for multiple Robertsonian rearrangements, a group of as many as fifteen chromosomes may line up together during meiosis (Capanna et al. 1976). In this situation the chromosomes will not separate properly, and the individual will probably be sterile (Gropp and Winking 1981).&#8221;

There is a family located with 44 chromosomes that have had such chronic problems.

Balanced translocations and Down syndrome

 

[Zaius137]

It is being found that the major differences between chimps and humans are not in the individual SNP’s but rather in genetic switches. How did these preexisting switches come to be and if evolution is right how were they retained? Evolution has no satisfactory explanation to date. Common design on the other hand predicts such switches.

http://www.pbs.org/wgbh/nova/evolution/dna-human-evolution.html