CB144: Human and chimp genomes differ by more than one percent.
Mark Isaak
release this now:
--------------------------
Claim CB144. Human and chimp genomes differ by more than one percent.
For years, evolutionists have hailed the chimpanzee as "our closest
living relative" and have pointed out that the DNA is 98 to 99 percent
identical between the two. Scientists now say the difference is 4
percent, double what they have been claiming for years.
Source:
DeWitt, David A. 2005. Chimp genome sequence very different from man.
http://www.answersingenesis.org/docs2005/0905chimp.asp
Response:
1. The difference between chimpanzees and humans due to
single-nucleotide substitutions averages 1.23 percent, of which 1.06
percent or less is due to fixed divergence, and the rest being a
result of polymorphism within chimp populations and within human
populations. Insertion and deletion (indel) events account for
another approximately 3 percent difference between chimp and human
sequences, but each indel typically involves multiple nucleotides.
The number of genetic changes from indels is a fraction of the number
of single-nucleotide substitutions (roughly 5 million compared with
roughly 35 million). So describing humans and chimpanzees as 98 to 99
percent identical is appropriate (Chimpanzee Sequencing 2005).
References:
1. Chimpanzee Sequencing and Analysis Consortium. 2005. Initial
sequence of the chimpanzee genome and comparison with the human
genome. _Nature_ 437: 69-87.
--
Mark Isaak eciton (at) earthlink (dot) net
"Voice or no voice, the people can always be brought to the bidding of
the leaders. That is easy. All you have to do is tell them they are
being attacked, and denounce the pacifists for lack of patriotism and
exposing the country to danger." -- Hermann Goering
John Harshman
Looks good to me. You might also consider Roy Britten's paper in which
he announced a 5% difference, using the same measure as the 4% above,
but in a genome region that turns out to have more indels than the
average over the whole genome. And you might expand in two ways:
1. There are all sorts of ways to measure genetic difference, depending
on what parts of the genome you count and how you count them. In this
way, you can get all sorts of different numbers for the same pair of
species. Human-chimp comparisons can run between 0% and 5% difference,
depending on how you count.
2. When comparing estimates for different pairs of species, it's
essential to use the same measure; otherwise you are doing the
equivalent of comparing inches to feet. Practices like this, using
different measures, are how some creationists have managed to come up
with humans being closer to mice (or pigs, or even fruit flies) than to
humans. If you use the same measure for each comparison, chimps will
always be closer to humans than are any other species.
The Last Conformist
I assume that is supposed to say "chimps" or "apes". I've not yet
encountered a creationist who claims that mice, pigs, or fruit flies
are nested *within* H. sapiens, altho I suppose I should not be very
surprised if I were to.
adventu...@yahoo.com
If you could test the Neanderthal man Who was not the exact same
species as Homosapian but was the other Upright walking ape man we
killed 40,000 years ago I believe it would be much closer.
Two upright walking apeman exsisted on this planet.
Too bad we killed the closest match we had.
John Harshman
Been done. Of course they're much closer. Duh. But there are plenty of
other extinct, upright walking ape men, from H. heidelbergensis through
Ardipithecus. No DNA for any of them, though.
Mark Isaak
<jharshman....@pacbell.net> wrote:
>Mark Isaak wrote:
>
>> Claim CB144. Human and chimp genomes differ by more than one percent.
>>
>Looks good to me. You might also consider Roy Britten's paper in which
>he announced a 5% difference, using the same measure as the 4% above,
>but in a genome region that turns out to have more indels than the
>average over the whole genome. And you might expand in two ways:
>
>1. There are all sorts of ways to measure genetic difference, depending
>on what parts of the genome you count and how you count them. In this
>way, you can get all sorts of different numbers for the same pair of
>species. Human-chimp comparisons can run between 0% and 5% difference,
>depending on how you count.
You mentioned earlier a 0.5% different in protein-coding regions.
Have a reference?
I also vaguely recall that you can get much higher than 5% difference
if you count genes instead of bases, so that any difference in a gene
counts as a completely different gene. Any idea of numbers here?
John Harshman
> On Fri, 23 Sep 2005 21:51:05 GMT, John Harshman
> <jharshman....@pacbell.net> wrote:
>
>
>>Mark Isaak wrote:
>>
>>
>>>Claim CB144. Human and chimp genomes differ by more than one percent.
>>>
>>
>>Looks good to me. You might also consider Roy Britten's paper in which
>>he announced a 5% difference, using the same measure as the 4% above,
>>but in a genome region that turns out to have more indels than the
>>average over the whole genome. And you might expand in two ways:
>>
>>1. There are all sorts of ways to measure genetic difference, depending
>>on what parts of the genome you count and how you count them. In this
>>way, you can get all sorts of different numbers for the same pair of
>>species. Human-chimp comparisons can run between 0% and 5% difference,
>>depending on how you count.
>
>
> You mentioned earlier a 0.5% different in protein-coding regions.
> Have a reference?
Not immediately handy. And this is one of the few numbers that the chimp
genome paper does not report. I can give you mean divergence at
synonymous sites and mean divergence at non-synonymous sites, and from
this you could (by assuming the proportion of sites in either category)
estimate such a number, which by the way would turn out to be about
0.5%; but it's not reported directly.
> I also vaguely recall that you can get much higher than 5% difference
> if you count genes instead of bases, so that any difference in a gene
> counts as a completely different gene. Any idea of numbers here?
I recall this. What was being counted was the proportion of
protein-coding genes with at least one difference. Chimp genome paper to
the rescue: ". Orthologous proteins in human and chimpanzee are
extremely similar, with ~29% being identical and the typical orthologue
differing by only two amino acids, one per lineage." So there you have
it: chimps and humans are 71% different.
Mark Isaak
certainly nothing major. Paragraph 2 is new. I considered adding a
reference to Britten's 5% difference estimate, but I could not figure
out where it would fit in or why it is needed.
--------------------------
Claim CB144. Human and chimp genomes differ by more than one percent.
For years, evolutionists have hailed the chimpanzee as "our closest
living relative" and have pointed out that the DNA is 98 to 99 percent
identical between the two. Scientists now say the difference is 4
percent, double what they have been claiming for years.
Source:
DeWitt, David A. 2005. Chimp genome sequence very different from man.
http://www.answersingenesis.org/docs2005/0905chimp.asp
Response:
1. The difference between chimpanzees and humans due to
single-nucleotide substitutions averages 1.23 percent, of which 1.06
percent or less is due to fixed divergence, and the rest being a
result of polymorphism within chimp populations and within human
populations. Insertion and deletion (indel) events account for
another approximately 3 percent difference between chimp and human
sequences, but each indel typically involves multiple nucleotides.
The number of genetic changes from indels is a fraction of the number
of single-nucleotide substitutions (roughly 5 million compared with
roughly 35 million). So describing humans and chimpanzees as 98 to 99
percent identical is entirely appropriate (Chimpanzee Sequencing
2005).
2. The difference measurement depends on what you are measuring. If
you measure the number of proteins for which the entire protein is
identical in the two species, humans and chimpanzees are 29 percent
identical (Chimpanzee Sequencing 2005). If you measure nonsynonymous
base pair differences within protein coding regions, humans and chimps
are 99.45 percent identical (Chen et al. 2001). Whatever measure is
used, however, as long as the same measurement is used consistently,
will show that humans are more closely related to chimpanzees
(including the bonobo, sister species to the common chimpanzee) than
to any other species.
References:
1. Chen, F.-C., E. J. Vallender, H. Wang, C.-S. Tzeng, and W.-H. Li.
2001. Genomic divergence between human and chimpanzee estimated from
large-scale alignments of genomic sequences. _Journal of Heredity_
92(6): 481-489.
2. Chimpanzee Sequencing and Analysis Consortium. 2005. Initial
John Harshman
Memo to Steve Shaffner: is this really the way this paper is supposed to
be cited? It seems so weird.
> 2. The difference measurement depends on what you are measuring. If
> you measure the number of proteins for which the entire protein is
> identical in the two species, humans and chimpanzees are 29 percent
> identical (Chimpanzee Sequencing 2005). If you measure nonsynonymous
> base pair differences within protein coding regions, humans and chimps
> are 99.45 percent identical (Chen et al. 2001). Whatever measure is
> used, however, as long as the same measurement is used consistently,
> will show that humans are more closely related to chimpanzees
> (including the bonobo, sister species to the common chimpanzee) than
> to any other species.
>
> References:
>
> 1. Chen, F.-C., E. J. Vallender, H. Wang, C.-S. Tzeng, and W.-H. Li.
> 2001. Genomic divergence between human and chimpanzee estimated from
> large-scale alignments of genomic sequences. _Journal of Heredity_
> 92(6): 481-489.
> 2. Chimpanzee Sequencing and Analysis Consortium. 2005. Initial
> sequence of the chimpanzee genome and comparison with the human
> genome. _Nature_ 437: 69-87.
Good. You might want to mention that the old 98.5% figure comes from the
DNA hybridization experiments of Sibley & Ahlquist. It refers to the
mean sequence difference among those short segments (~500bp) of the
single-copy genome (repetitive elements removed) that are similar enough
to hybridize. Though that turns out to be pretty close to the figure you
get from the entire genome.
Mark Isaak
I saw it cited like that in a _Science_ article.
>> 2. The difference measurement depends on what you are measuring. If
>> you measure the number of proteins for which the entire protein is
>> identical in the two species, humans and chimpanzees are 29 percent
>> identical (Chimpanzee Sequencing 2005). If you measure nonsynonymous
>> base pair differences within protein coding regions, humans and chimps
>> are 99.45 percent identical (Chen et al. 2001). Whatever measure is
>> used, however, as long as the same measurement is used consistently,
>> will show that humans are more closely related to chimpanzees
>> (including the bonobo, sister species to the common chimpanzee) than
>> to any other species.
>>
>> References:
>>
>> 1. Chen, F.-C., E. J. Vallender, H. Wang, C.-S. Tzeng, and W.-H. Li.
>> 2001. Genomic divergence between human and chimpanzee estimated from
>> large-scale alignments of genomic sequences. _Journal of Heredity_
>> 92(6): 481-489.
>> 2. Chimpanzee Sequencing and Analysis Consortium. 2005. Initial
>> sequence of the chimpanzee genome and comparison with the human
>> genome. _Nature_ 437: 69-87.
>
>Good. You might want to mention that the old 98.5% figure comes from the
> DNA hybridization experiments of Sibley & Ahlquist. It refers to the
>mean sequence difference among those short segments (~500bp) of the
>single-copy genome (repetitive elements removed) that are similar enough
>to hybridize. Though that turns out to be pretty close to the figure you
>get from the entire genome.
Preliminary version, until I check it with what Sibley and Ahlquist
actually say:
2. The difference measurement depends on what you are measuring. If
you measure the number of proteins for which the entire protein is
identical in the two species, humans and chimpanzees are 29 percent
identical (Chimpanzee Sequencing 2005). If you measure nonsynonymous
base pair differences within protein coding regions, humans and chimps
are 99.45 percent identical (Chen et al. 2001). The original 98.5
percent estimate came from DNA hybridization experiments, which
measured (indirectly, via DNA melting temperature) sequence difference
among short segements of the genomes that are similar enough to
hybridize but with repetitive elements removed (Sibley and Ahlquist
1987). Whatever measure is used, however, as long as the same
measurement is used consistently, will show that humans are more
closely related to chimpanzees (including the bonobo, sister species
to the common chimpanzee) than to any other species.
References:
...
3. Sibley, C. G. and J. E. Ahlquist. 1987. DNA hybridization evidence
of hominid phylogeny: Results from an expanded data set. _Journal of
Molecular Evolution_ 26: 99-121.
John Harshman
Whoops, missed this one. Are you sure it's measuring nonsynonymous
differences only? That sounds like all differences to me. Nonsynonymous
ones should be considerably lower. In fact the chimp paper gives an
estimate of nonsynonymous differences as half that (0.245%).
> The original 98.5
> percent estimate came from DNA hybridization experiments, which
> measured (indirectly, via DNA melting temperature) sequence difference
> among short segements of the genomes that are similar enough to
> hybridize but with repetitive elements removed (Sibley and Ahlquist
> 1987). Whatever measure is used, however, as long as the same
> measurement is used consistently, will show that humans are more
> closely related to chimpanzees (including the bonobo, sister species
> to the common chimpanzee) than to any other species.
That's correct. (Though I think it might actually have been 98.6%, it's
been generally rounded off.)
Mark Isaak
<jharshman....@pacbell.net> wrote:
>Mark Isaak wrote:
>[...]
>> 2. The difference measurement depends on what you are measuring. If
>> you measure the number of proteins for which the entire protein is
>> identical in the two species, humans and chimpanzees are 29 percent
>> identical (Chimpanzee Sequencing 2005). If you measure nonsynonymous
>> base pair differences within protein coding regions, humans and chimps
>> are 99.45 percent identical (Chen et al. 2001).
>
>Whoops, missed this one. Are you sure it's measuring nonsynonymous
>differences only? That sounds like all differences to me. Nonsynonymous
>ones should be considerably lower. In fact the chimp paper gives an
>estimate of nonsynonymous differences as half that (0.245%).
From the abstract of Chen et al.:
"Annotated coding and noncoding regions of homologous chimpanzee genes
were also retrieved from GenBank and compared. The average synonymous
and nonsynonymous divergences in 88 coding genes are 1.48% and 0.55%,
respectively."
It was the only estimate I found online (probably because I stopped
looking when I found it). Do you have a page number handy for where
the 0.245% estimate is in the chimp genome paper?
John Harshman
> On Tue, 27 Sep 2005 18:26:49 GMT, John Harshman
> <jharshman....@pacbell.net> wrote:
>
>
>>Mark Isaak wrote:
>>[...]
>>
>>>2. The difference measurement depends on what you are measuring. If
>>>you measure the number of proteins for which the entire protein is
>>>identical in the two species, humans and chimpanzees are 29 percent
>>>identical (Chimpanzee Sequencing 2005). If you measure nonsynonymous
>>>base pair differences within protein coding regions, humans and chimps
>>>are 99.45 percent identical (Chen et al. 2001).
>>
>>Whoops, missed this one. Are you sure it's measuring nonsynonymous
>>differences only? That sounds like all differences to me. Nonsynonymous
>>ones should be considerably lower. In fact the chimp paper gives an
>>estimate of nonsynonymous differences as half that (0.245%).
>
>
> From the abstract of Chen et al.:
> "Annotated coding and noncoding regions of homologous chimpanzee genes
> were also retrieved from GenBank and compared. The average synonymous
> and nonsynonymous divergences in 88 coding genes are 1.48% and 0.55%,
> respectively."
That matches the synonymous differences in the chimp paper, but is twice
the nonsynonymous total. I wonder what that means.
> It was the only estimate I found online (probably because I stopped
> looking when I found it). Do you have a page number handy for where
> the 0.245% estimate is in the chimp genome paper?
It doesn't appear in quite that form. You have to construct it from the
table in figure 9, page 76, by adding together the two KsubA branch
lengths. Unfortunately, you can't figure out the total percent
difference unless you know the proportion of non-synonymous and
synonymous sites. If synonymous sites are about 1/3 of the total (which
should be fairly close), then the total percent difference is (2/3 *
0.235) + (1/3 * 1.419 = 0.636), close to what I remembered.
Mark Isaak
<jharshman....@pacbell.net> wrote:
Correcting math and/or copying errors: (2/3 * 0.245) + (1/3 * 1.219) =
0.570
Anyway, I will go with 0.245% and add the following paragraph at the
end:
Note also, though, that evolution has not been uniform throughout
the genomes, so estimates of human-chimp divergence which consider
only part of the genome can give different results (Britten 2002, Chen
et al. 2001).
Steve Schaffner
> Mark Isaak wrote:
>
> >>>percent identical is entirely appropriate (Chimpanzee Sequencing
> >>>2005).
> >>
> >>Memo to Steve Shaffner: is this really the way this paper is supposed to
> >>be cited? It seems so weird.
Beats me -- that's what Pubmed and EndNote are for. The official
author string is Chimpanzee Seqeuencing and Analysis Consortium.
--
Steve Schaffner s...@broad.mit.edu
Immediate assurance is an excellent sign of probable lack of
insight into the topic. Josiah Royce