Are Humans Really Genetically Close to Apes? [Yes]

[Oxymoron]

[Admin Edit:]
From the original paper, the 98% figure is still accurate.

As expected, we found that the degree of similarity between orthologous chimpanzee and human MSY sequences (98.3% nucleotide identity) differs only modestly from that reported when comparing the rest of the chimpanzee and human genomes (98.8%). Surprisingly, however, > 30% of chimpanzee MSY sequence has no homologous, alignable counterpart in the human MSY, and vice versa (Supplementary Fig. 8 and Supplementary Note 3). In this respect the MSY differs radically from the remainder of the genome, where < 2% of chimpanzee euchromatic sequence lacks an homologous, alignable counterpart in humans, and vice versa. We conclude that, since the separation of the chimpanzee and human lineages, sequence gain and loss have been far more concentrated in the MSY than in the balance of the genome.

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http://dspace.mit.edu/openaccess-disseminate/1721.1/59332

Original (incorrect) post follows:

So much for the DNA being 98% the same for apes and man.

http://www.johnhawks.net/weblog/reviews/chimpanzees/genetics/chimpanzee-y-chromosome-2010.html

This is from a new paper that's just shown up in the Nature advance publication zone. The authors are Jennifer Hughes and colleagues, and the subject is the first complete sequencing of the chimpanzee Y chromosome. "MSY" stands for "male-specific region of the Y chromosome" -- it's most of the Y, aside from a small fraction that recombines with the X chromosome.

More than thirty percent of the chimpanzee Y chromosome has no homolog in humans, and likewise for the human Y in chimpanzees.
I mean, really -- here's a map:

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[David Fraser]

So much for the DNA being 98% the same for apes and man.

http://www.johnhawks.net/weblog/reviews/chimpanzees/genetics/chimpanzee-y-chromosome-2010.html

This is from a new paper that's just shown up in the Nature advance publication zone. The authors are Jennifer Hughes and colleagues, and the subject is the first complete sequencing of the chimpanzee Y chromosome. "MSY" stands for "male-specific region of the Y chromosome" -- it's most of the Y, aside from a small fraction that recombines with the X chromosome.

More than thirty percent of the chimpanzee Y chromosome has no homolog in humans, and likewise for the human Y in chimpanzees.
I mean, really -- here's a map:

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98% + of bonded pairs of DNA are the same. However the DNA is organised in the chromosomes so it is not surprising there are chromosomal differences

 

[solrey]

The author of that blog post apparently failed to find and read the whole paper. The new findings do not change the fact that chimp and human DNA is more than 98% the same.

As expected, we found that the degree of similarity between orthologous chimpanzee and human MSY sequences (98.3% nucleotide identity) differs only modestly from that reported when comparing the rest of the chimpanzee and human genomes (98.8%). Surprisingly, however, > 30% of chimpanzee MSY sequence has no homologous, alignable counterpart in the human MSY, and vice versa (Supplementary Fig. 8 and Supplementary Note 3). In this respect the MSY differs radically from the remainder of the genome, where < 2% of chimpanzee euchromatic sequence lacks an homologous, alignable counterpart in humans, and vice versa. We conclude that, since the separation of the chimpanzee and human lineages, sequence gain and loss have been far more concentrated in the MSY than in the balance of the genome.

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http://dspace.mit.edu/openaccess-disseminate/1721.1/59332

 

[O_O]

...

[facepalm]

 

[solrey]

[facepalm]

More like...

 

[Oxymoron]

98% + of bonded pairs of DNA are the same. However the DNA is organised in the chromosomes so it is not surprising there are chromosomal differences

So the DNA is 98% the same but 30% of the chromosomes are wildly different... but that is unimportant/unsurprising?

[...]

http://answers.yahoo.com/question/index?qid=20091007101242AAd0lhA

DNA is a chemical consisting of an enormously-long chain of similar molecules called "bases". DNA is a "double helix" which means it has two strands wrapped around each other. At each point along it, we find bases linked to each other from one strand to the other. Those are "base pairs".

A set of three bases on a single strand of DNA is called a "codon". This is because it codes for a particular amino acid when the codon is transferred to RNA and then used to construct a protein.

A long string of such codons, starting with what is called a "promoter site" and ending at a "stop codon" is what we call a "gene". It maps from DNA to a particular protein that that DNA codes for.

A chromosome is a (usually huge) collection of genes (plus some "non-coding DNA") which are linked into a single molecule.

While bacteria normally have only one chromosome whose structure is a closed loop, eukaryotes usually have multiple chromosomes consisting of open-ended strings of DNA. The eukaryotic chromosomes are generally much larger.

The number of chromosomes varies a lot and doesn't seem to relate much to the complexity of the organism. Humans have 23 pairs or a total of 46 chromosomes (including one mismatched pair if you are male). The whole set of chromosomes is referred to as the organism's "genome".

So, in order of increasing scale, we have: base - codon - gene - chromosome - genome.

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"The Blogger", is not 'just some guy', he is a professor with years of experience... and he finds the vast changes over such a short period remarkable, as do I.

http://www.johnhawks.net/weblog/hawks/hawks.html

I'm an anthropologist, and I study the bones and genes of ancient humans. I've worked on almost every part of our evolutionary story, from the very origin of our lineage among the apes up to the last 10,000 years of our history.

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My academic position is Professor of Anthropology at the University of Wisconsin—Madison. Right now, I'm Associate Chair of Anthropology, a Howard Hughes Medical Institute (HHMI) Faculty Fellow, and an associate member of both the Department of Zoology and the J. F. Crow Institute for the Study of Evolution. I'm the recent recipient of the UW's H. I. Romnes Faculty Fellowship and its Vilas Associate award. I've been at the University since 2002.

My work has taken me to Africa, Asia, and Europe, where I have measured thousands of bones and investigated dozens of archaeological sites. In my lab, we work with the bioinformatics of whole genome sequences from hundreds of living people (and a few ancient ones) to uncover the patterns of relationships that connect them. I'm an expert in population dynamics and the process of natural selection on both genes and morphological traits. I've used my work in genetics and skeletal biology to form rich collaborations with colleagues in a dozen countries.

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[Marcus Mudd]

What we can all agree on is that understanding how genetics manifests itself as traits, and how these differ from our supposed closest relatives in the animal kingdom is not simple!

ive been researching this topic and following this conversation, the face palms are completely unneccesary as the topic is so convoluted that I can bet none of us fully understand.

my research has garnished ideas from both sides of this argument, there are articles that view the 98% identical nature of chimp/human DNA is specifically protein based, whereas the portions of dna responsible for protein creation and the proteins themselves are identical. Ive also read that all male specific nucleotide sequences were identical, but the proteins that regulated mental activity were significantly different. I don't understand all of the information, but I am not convinced that this evidence proves humans evolved from apes.

of course this is another evolution thread in disguise so with that said protein creation regulated by dna itself is evidence for a creator, due to the complexity of the amino acid patterns and the specific actions they portray in activating and deactivating gene expression. proteins are biologcal nanotechnology and nano technology can in no way emerge from nothing.

 

[Mick West]

Given that Chimps are genetically more complex than humans, wouldn't that then suggest that chimps evolved from humans, and not the other way around?

http://www.nbcnews.com/science/chimp-genetic-history-more-complex-humans-6C10533510

Surprisingly, Marques-Bonet said, the genetic history of chimpanzees turned out to be much more complex than that of humans. Compared with chimps, "it looks like our (humans') history has been really simple," Marques-Bonet said. Human populations encountered a bottleneck when they left Africa, and have since expanded to colonize the whole planet. By contrast, chimpanzee populations have undergone at least two to three bottlenecks and expansions, Marques-Bonet said.

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More likely, some chimp alien/god came along 5 million year ago, and though early hominids could do with some tweaking, so created chimps. Just didn't work out as they expected.

 

[Oxymoron]

Given that Chimps are genetically more complex than humans, wouldn't that then suggest that chimps evolved from humans, and not the other way around?

http://www.nbcnews.com/science/chimp-genetic-history-more-complex-humans-6C10533510

Surprisingly, Marques-Bonet said, the genetic history of chimpanzees turned out to be much more complex than that of humans. Compared with chimps, "it looks like our (humans') history has been really simple," Marques-Bonet said. Human populations encountered a bottleneck when they left Africa, and have since expanded to colonize the whole planet. By contrast, chimpanzee populations have undergone at least two to three bottlenecks and expansions, Marques-Bonet said.

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More likely, some chimp alien/god came along 5 million year ago, and though early hominids could do with some tweaking, so created chimps. Just didn't work out as they expected.

Lol... Nice to see you finally getting the hang of this debunking game Mick

But seriously, the diversity of expert opinion on it is interesting.

I personally like the 2001 Space Odyssey scenario but really I am just posting here on the 'general discussion' because i think it is an interesting subject which as Marcus said, no one really understands.

Despite the genetic similarity between humans and chimpanzees, the two species are clearly quite different. Some scientists had hypothesized that the differences stem from the "lost" parts of human genomes compared with chimp genomes. But the new study disproved that theory by showing that the lost parts were mostly nonfunctional.

So if it's not genetics, what makes humans different from their great-ape cousins? "If I knew, I would have the Nobel Prize," Marques-Bonet said.

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I am not out to upset anyone here, I just think it good to question things to the best of our ability and perhaps we can all learn a thing or two.

 

[solrey]

So the DNA is 98% the same but 30% of the chromosomes are wildly different... but that is unimportant/unsurprising?

Isn't that like saying 'a mud hut is made from ceramics and so is the Taj Mahal, so they are not dissimilar?

http://answers.yahoo.com/question/index?qid=20091007101242AAd0lhA

"The Blogger", is not 'just some guy', he is a professor with years of experience... and he finds the vast changes over such a short period remarkable, as do I.

http://www.johnhawks.net/weblog/hawks/hawks.html

I simply said, "The author of that blog post...", I did not say the blogger was 'just some guy', so why use quote marks like that? I take that as a form of ad-hom, an attempt to discredit my comment by implying that it was demeaning. Putting words into peoples mouths is an ugly habit, I kindly suggest you refrain from such practices.

His interpretation of the paper was incorrect and he seemed to not have read more than the abstract so I didn't waste any time looking into the authors background... instead I read the damn paper and understood it, what a novel idea.

The 30% difference is for ONE chromosome from the mis-matched pair, not all 23 pairs of 46 chromosomes. As the paper states...

In this respect the MSY differs radically from the remainder of the genome, where < 2% of chimpanzee euchromatic sequence lacks an homologous, alignable counterpart in humans, and vice versa. We conclude that, since the separation of the chimpanzee and human lineages, sequence gain and loss have been far more concentrated in the MSY than in the balance of the genome.

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In other words, the majority of that <2% overall difference mostly resides within the one chromosome, the oddball, in males only. MSY is the male-specific region of the Y chromosome, which is composed of nearly 50 million base pairs. Considering the rest of the genome is nearly identical, that 30% difference in one male specific chromosome is literally just a drop in the bucket.

 

[Oxymoron]

I simply said, "The author of that blog post...", I did not say the blogger was 'just some guy', so why use quote marks like that? I take that as a form of ad-hom, an attempt to discredit my comment by implying that it was demeaning. Putting words into peoples mouths is an ugly habit, I kindly suggest you refrain from such practices.

Well that is a bit strong IMO, especially coming from the poster of a chimp facepalming. Like I said, quite deliberately, my intent is not to upset anyone but simply to explore some wide ranging views on a very complex subject, so please accept my apology for any perceived offence and be assured it was not intended.

"The author of that blog" paraphrases very well to 'The blogger'... so I think you are over reacting.

Are you heavily invested in some way in the evolution concept?

His interpretation of the paper was incorrect and he seemed to not have read more than the abstract so I didn't waste any time looking into the authors background... instead I read the damn paper and understood it, what a novel idea.

The 30% difference is for ONE chromosome from the mis-matched pair, not all 23 pairs of 46 chromosomes. As the paper states...

In this respect the MSY differs radically from the remainder of the genome, where < 2% of chimpanzee euchromatic sequence lacks an homologous, alignable counterpart in humans, and vice versa. We conclude that, since the separation of the chimpanzee and human lineages, sequence gain and loss have been far more concentrated in the MSY than in the balance of the genome.

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In other words, the majority of that <2% overall difference mostly resides within the one chromosome, the oddball, in males only. MSY is the male-specific region of the Y chromosome, which is composed of nearly 50 million base pairs. Considering the rest of the genome is nearly identical, that 30% difference in one male specific chromosome is literally just a drop in the bucket.

If it is the case that 'it doesn't matter' ("a drop in the bucket), then I doubt whether such an experienced expert would make such a deal out of it.

You can always take it up with him personally if you wish. I am 'just some guy', trying to get my head around it so it is pointless taking me to task on it. I know that a number of posters on here like to post on sites they disagree with so that seems the best option really.

BTW, I was mostly responding to Dave anyway, as he was/is of the opinion that it is unimportant in the scheme of things.

However, I am aware that The genetic code consists of 64 triplets of nucleotides and only 20 amino acids, which really means that there is very little that any known life can deviate genetically given such a small base code and small number of amino acids. It therefore seems logical to me, (but I may be wrong), that differences found in species appear to be derived in the way these building blocks are put together, more than what they are.

http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/C/Codons.html

Second nucleotide
UCAG
U UUU Phenylalanine (Phe)UCU Serine (Ser)UAU Tyrosine (Tyr)UGU Cysteine (Cys)U
UUC PheUCC SerUAC TyrUGC CysC
UUA Leucine (Leu)UCA Ser UAA STOPUGA STOPA
UUG LeuUCG Ser UAG STOPUGG Tryptophan (Trp)G
C CUU Leucine (Leu)CCU Proline (Pro)CAU Histidine (His) CGU Arginine (Arg)U
CUC LeuCCC ProCAC HisCGC Arg C
CUA LeuCCA ProCAA Glutamine (Gln)CGA Arg A
CUG LeuCCG ProCAG GlnCGG Arg G
A AUU Isoleucine (Ile)ACU Threonine (Thr)AAU Asparagine (Asn)AGU Serine (Ser)U
AUC IleACC ThrAAC AsnAGC Ser C
AUA IleACA Thr AAA Lysine (Lys)AGA Arginine (Arg)A
AUG Methionine (Met) or STARTACG ThrAAG LysAGG Arg G
G GUU Valine ValGCU Alanine (Ala)GAU Aspartic acid (Asp)GGU Glycine (Gly)U
GUC (Val)GCC AlaGAC AspGGC GlyC
GUA ValGCA AlaGAA Glutamic acid (Glu)GGA GlyA
GUG ValGCG AlaGAG GluGGG GlyG

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[Mick West]

I was reading "The Crowd: A Study of the popular Mind" (1895) today, and I came across this interesting comment:

The biological sciences have been transformed since embryology has shown the immense influence of the past on the evolution of living beings

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1895 being pre-DNA, I thought it was interesting, back in the day the similarity between species could be measured to some extent by the speed of divergence of the embryo. The more human-like the animal, the more similar the early stages, even fish look like humans at early stages of embryo development

 

[Marcus Mudd]

'looks like a fish' is not science.

 

[Mick West]

'looks like a fish' is not science.

It's direct empirical evidence. It's not the only evidence, but it's certainly consistent with the other evidence of common descent, and genetic closeness.

 

[Oxymoron]

More on the differences, highlight added. It is basically the same data but it does highlight the significance, which has largely been downplayed here.

http://www.ncbi.nlm.nih.gov/pubmed/20072128

The human Y chromosome began to evolve from an autosome hundreds of millions of years ago, acquiring a sex-determining function and undergoing a series of inversions that suppressed crossing over with the X chromosome. Little is known about the recent evolution of the Y chromosome because only the human Y chromosome has been fully sequenced. Prevailing theories hold that Y chromosomes evolve by gene loss, the pace of which slows over time, eventually leading to a paucity of genes, and stasis. These theories have been buttressed by partial sequence data from newly emergent plant and animal Y chromosomes, but they have not been tested in older, highly evolved Y chromosomes such as that of humans. Here we finished sequencing of the male-specific region of the Y chromosome (MSY) in our closest living relative, the chimpanzee, achieving levels of accuracy and completion previously reached for the human MSY. By comparing the MSYs of the two species we show that they differ radically in sequence structure and gene content, indicating rapid evolution during the past 6 million years. The chimpanzee MSY contains twice as many massive palindromes as the human MSY, yet it has lost large fractions of the MSY protein-coding genes and gene families present in the last common ancestor. We suggest that the extraordinary divergence of the chimpanzee and human MSYs was driven by four synergistic factors: the prominent role of the MSY in sperm production, 'genetic hitchhiking' effects in the absence of meiotic crossing over, frequent ectopic recombination within the MSY, and species differences in mating behaviour. Although genetic decay may be the principal dynamic in the evolution of newly emergent Y chromosomes, wholesale renovation is the paramount theme in the continuing evolution of chimpanzee, human and perhaps other older MSYs.

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[Dan Wilson]

Just to illustrate the size of the Y chromosome in comparison to a whole genome:

The Y chromosome is the little guy in the bottom right-hand corner, paired with the larger X chromosome.
So 30% of a specific region in that little nub is what the paper is discussing.