From Science Daily, “Humans, Chimpanzees and Monkeys Share DNA but Not Gene Regulatory Mechanisms”

_{Denyse O'Leary

November 6, 2012

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Science Daily features an interesting report today, which you can read here:

Humans share over 90% of their DNA with their primate cousins. The expression or activity patterns of genes differ across species in ways that help explain each species’ distinct biology and behavior.

DNA factors that contribute to the differences were described on Nov. 6 at the American Society of Human Genetics 2012 meeting in a presentation by Yoav Gilad, Ph.D., associate professor of human genetics at the University of Chicago.

Dr. Gilad reported that up to 40% of the differences in the expression or activity patterns of genes between humans, chimpanzees and rhesus monkeys can be explained by regulatory mechanisms that determine whether and how a gene’s recipe for a protein is transcribed to the RNA molecule that carries the recipe instructions to the sites in cells where proteins are manufactured.

Read the rest here.

Comments

This yEC says again that DNA likeness does not equal biological relatedness. We were created in gods image and simply given the best type of body on earth for fun and profit. These percentage things are still hinting it matters how close in determining if related. If even they bred a ape with a human the result would still be a human 100% and in no way have ape intelligence. I welcome our bodies being as close as possible to a ape body because it could only be that way, looks that way, and doesn't matter one bit.Robert Byers_{November 7, 2012
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BA77: Thanks for the citations. Will be interesting to see if these hold up. As I think some have long suspected, the "98% similarity" (or 97% or 99% or whatever is often cited) is another of the evolutionary myths and follows a familiar pattern -- put forward on very slim evidence in order to prop up a desired narrative. Now in some cases it may have been innocent, based, for example, on the old, facile, idea that all that matters is gene-producing sequences and that their location and positioning don't matter. In other instances, there seems to have been a bit more deliberate reporting of the "favorable" numbers.Eric Anderson_{November 7, 2012
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Thank you, however that is still not a complete side-by-side comparison. But if that is any indication then the "over 90%" is wrong too.Joe_{November 7, 2012
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Actually Joe I left this one early study out, Do Human and Chimpanzee DNA Indicate an Evolutionary Relationship? Excerpt: Today, however, we have the majority of the human genome sequences, practically all of which have been released and made public. This allows scientists to compare every single nucleotide base pair between humans and primates—something that was not possible prior to the human genome project. In January 2002, a study was published in which scientists had constructed and analyzed a first-generation human chimpanzee comparative genomic map. This study compared the alignments of 77,461 chimpanzee bacterial artificial chromosome (BAC) end sequences to human genomic sequences. Fujiyama and colleagues “detected candidate positions, including two clusters on human chromosome 21, that suggest large, nonrandom regions of differences between the two genomes” (2002, 295:131). In other words, the comparison revealed some “large” differences between the genomes of chimps and humans. Amazingly, the authors found that only 48.6% of the whole human genome matched chimpanzee nucleotide sequences. [Only 4.8% of the human Y chromosome could be matched to chimpanzee sequences.] This study compared the alignments of 77,461 chimpanzee sequences to human genomic sequences obtained from public databases. Of these, 36,940 end sequences were unable to be mapped to the human genome (295:131). Almost 15,000 of those sequences that did not match human sequences were speculated to “correspond to unsequenced human regions or are from chimpanzee regions that have diverged substantially from humans or did not match for other unknown reasons” (295:132). http://www.apologeticspress.org/articles/2070bornagain77_{November 7, 2012
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No one knows what the genetic difference between chimps and humans is because no one has done a complete side-by-side comparison.Joe_{November 7, 2012
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Study Reports a Whopping "23% of Our Genome" Contradicts Standard Human-Ape Evolutionary Phylogeny - Casey Luskin - June 2011 Excerpt: For about 23% of our genome, we share no immediate genetic ancestry with our closest living relative, the chimpanzee. This encompasses genes and exons to the same extent as intergenic regions. We conclude that about 1/3 of our genes started to evolve as human-specific lineages before the differentiation of human, chimps, and gorillas took place. (of note; 1/3 of our genes is equal to about 7000 genes that we do not share with chimpanzees) http://www.evolutionnews.org/2011/06/study_reports_a_whopping_23_of047041.html Peer-Reviewed Paper in Medical Journal Challenges Evolutionary Science and Inaccurate Evolution-Education - Casey Luskin - January, 2012 Excerpt: DNA homology between ape and man has been reported to be 96% when considering only the current protein-mapping sequences, which represent only 2% of the total genome. However, the actual similarity of the DNA is approximately 70% to 75% when considering the full genome, including the previously presumed "junk DNA," which has now been demonstrated to code for supporting elements in transcription or expression. The 25% difference represents almost 35 million single nucleotide changes and 5 million insertions or deletions. http://www.evolutionnews.org/2012/01/peer-reviewed_p055221.html A simple statistical test for the alleged “99% genetic identity” between humans and chimps - September 2010 Excerpt: The results obtained are statistically valid. The same test was previously run on a sampling of 1,000 random 30-base patterns and the percentages obtained were almost identical with those obtained in the final test, with 10,000 random 30-base patterns. When human and chimp genomes are compared, the X chromosome is the one showing the highest degree of 30BPM similarity (72.37%), while the Y chromosome shows the lowest degree of 30BPM similarity (30.29%). On average the overall 30BPM similarity, when all chromosomes are taken into consideration, is approximately 62%. https://uncommondescent.com/intelligent-design/a-simple-statistical-test-for-the-alleged-99-genetic-identity-between-humans-and-chimps/ Do Human and Chimpanzee DNA Indicate an Evolutionary Relationship? Excerpt: the authors found that only 48.6% of the whole human genome matched chimpanzee nucleotide sequences. [Only 4.8% of the human Y chromosome could be matched to chimpanzee sequences.] http://www.apologeticspress.org/articles/2070 Recent Genetic Research Shows Chimps More Distant From Humans,,, - Jan. 2010 Excerpt: A Nature paper from January, 2010 titled, "Chimpanzee and human Y chromosomes are remarkably divergent in structure and gene content," found that Y chromosomes in humans and chimps "differ radically in sequence structure and gene content," showing "extraordinary divergence" where "wholesale renovation is the paramount theme.",,, “Even more striking than the gene loss is the rearrangement of large portions of the chromosome. More than 30% of the chimp Y chromosome lacks an alignable counterpart on the human Y chromosome, and vice versa,,," http://www.evolutionnews.org/2010/04/recent_genetic_research_shows.html The Gorilla Who Broke the Tree - Doug Axe PhD. - March 2012 Excerpt: Well, the recent publication of the gorilla genome sequence shows that the expected pattern just isn’t there. Instead of a nested hierarchy of similarities, we see something more like a mosaic. According to a recent report [1], “In 30% of the genome, gorilla is closer to human or chimpanzee than the latter are to each other…” That’s sufficiently difficult to square with Darwin’s tree that it ought to bring the whole theory into question. And in an ideal world where Darwinism is examined the way scientific theories ought to be examined, I think it would. But in the real world things aren’t always so simple. http://www.biologicinstitute.org/post/19703401390/the-gorilla-who-broke-the-tree From Jerry Coyne, More Table-Pounding, Hand-Waving - May 2012 Excerpt: "More than 6 percent of genes found in humans simply aren't found in any form in chimpanzees. There are over fourteen hundred novel genes expressed in humans but not in chimps." Jerry Coyne - ardent and 'angry' neo-Darwinist - professor at the University of Chicago in the department of ecology and evolution for twenty years. He specializes in evolutionary genetics. Dr. Fazale Rana states the chimp genome is about 12% larger than the human genome.
bornagain77_{November 7, 2012
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I've got papers which have percentage similarity all over the place: here are a few of my notes along that line:
The Demise of Junk DNA and Why It Matters - Jonathan M. - September 2012 Excerpt: “the prized 98% sequence-identify figure between humans and chimpanzees relates to the 2% of DNA that codes for the production of proteins. The non-protein-coding (Junk) regions of DNA are far more species-specific.,,, these (Junk) stretches of non-coding DNA really are functional, then what becomes of this (98%) sequence-identity figure and its significance with respect to shared ancestry?” http://www.evolutionnews.org/2012/09/the_demise_of_j_1064061.html Chimp chromosome creates puzzles - 2004 Excerpt: However, the researchers were in for a surprise. Because chimps and humans appear broadly similar, some have assumed that most of the differences would occur in the large regions of DNA that do not appear to have any obvious function. But that was not the case. The researchers report in 'Nature' that many of the differences were within genes, the regions of DNA that code for proteins. 83% of the 231 genes compared had differences that affected the amino acid sequence of the protein they encoded. And 20% showed "significant structural changes". In addition, there were nearly 68,000 regions that were either extra or missing between the two sequences, accounting for around 5% of the chromosome.,,, "we have seen a much higher percentage of change than people speculated." The researchers also carried out some experiments to look at when and how strongly the genes are switched on. 20% of the genes showed significant differences in their pattern of activity. http://www.nature.com/news/1998/040524/full/news040524-8.html Guy Walks Into a Bar and Thinks He's a Chimpanzee: The Unbearable Lightness of Chimp-Human Genome Similarity Excerpt: One can seriously call into question the statement that human and chimp genomes are 99% identical. For one thing, it has been noted in the literature that the exact degree of identity between the two genomes is as yet unknown (Cohen, J., 2007. Relative differences: The myth of 1% Science 316: 1836.). ,,, In short, the figure of identity that one wants to use is dependent on various methodological factors. http://www.evolutionnews.org/2009/05/guy_walks_into_a_bar_and_think.html Chimpanzee? 10-10-2008 - Dr Richard Buggs - research geneticist at the University of Florida ...Therefore the total similarity of the genomes could be below 70%. http://www.idnet.com.au/files/pdf/Chimpanzee.pdf DNA Comparisons between Humans and Chimps - Fazale Rana Excerpt: It is interesting that when evolutionary biologists discuss genetic comparisons between human and chimpanzee genomes, the fact that, again, as much as 25 percent of the two genomes won’t align receives no mention. Instead, the focus is only on the portions of the genome that display a high-degree of similarity. This distorted emphasis makes the case for the evolutionary connection between humans and chimps seem more compelling than it may actually be. http://www.reasons.org/dna-comparisons-between-humans-and-chimps-response-venema-critique-rtb-human-origins-model-part-2 Genomic monkey business - similarity re-evaluated using omitted data - by Jeffrey Tomkins and Jerry Bergman Excerpt: A review of the common claim that the human and chimpanzee (chimp) genomes are nearly identical was found to be highly questionable solely by an analysis of the methodology and data outlined in an assortment of key research publications.,,, Based on the analysis of data provided in various publications, including the often cited 2005 chimpanzee genome report, it is safe to conclude that human–chimp genome similarity is not more than ~87% identical, and possibly not higher than 81%. These revised estimates are based on relevant data omitted from the final similarity estimates typically presented.,,, Finally, a very recent large-scale human–chimp genome comparison research report spectacularly confirms the data presented in this report. The human–chimp common ancestor paradigm is clearly based more on myth and propaganda than fact. http://creation.com/human-chimp-dna-similarity-re-evaluated
bornagain77_{November 7, 2012
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Over on the other thread, wd400 told us it was, what, less than 2% difference? Whatever happened to 99% the same, 98% the same, and so on?
Primates. They weren't specifically saying chimps/bonobos which is commonly cited at 4-5% when indels are counted. However, I've heard some creationists cite this line:
According to the Genome Size Database (http://www.genomesize.com), the human genome size (reported as "C-value", a unit of weight that's theoretically directly proportional to genome size) is 3.2. Chimp C-values have been recorded as 3.46, 3.63, 3.76, and 3.85. They all indicate the human genome is smaller (8–17%)
Is this a reliable metric?JoeCoder_{November 7, 2012
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This can't be right.
Humans share over 90% of their DNA with their primate cousins.
Over on the other thread, wd400 told us it was, what, less than 2% difference? Whatever happened to 99% the same, 98% the same, and so on? ------ Good research, though. I expect the role of regulatory material (both in DNA and outside of DNA) will be shown to have more and more function as time goes on. The whole system is built upon regulation and coordinated function. The old Central Dogma of DNA -> RNA -> protein -> function is becoming less and less useful every day.Eric Anderson_{November 7, 2012
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Related notes:
The mouse is not enough - February 2011 Excerpt: Richard Behringer, who studies mammalian embryogenesis at the MD Anderson Cancer Center in Texas said, “There is no ‘correct’ system. Each species is unique and uses its own tailored mechanisms to achieve development. By only studying one species (eg, the mouse), naive scientists believe that it represents all mammals.” http://www.the-scientist.com/news/display/57986/ Modern Synthesis of Neo-Darwinism Is Dead - No Evidence For Body Plan Morphogenesis From Embryonic Mutations - Paul Nelson - video http://www.metacafe.com/watch/5548184/ First Decoded Marsupial Genome Reveals "Junk DNA" Surprise - 2007 Excerpt: In particular, the study highlights the genetic differences between marsupials such as opossums and kangaroos and placental mammals like humans, mice, and dogs. ,,, The researchers were surprised to find that placental and marsupial mammals have largely the same set of genes for making proteins. Instead, much of the difference lies in the (regulatory) controls that turn genes on and off. http://news.nationalgeographic.com/news/2007/05/070510-opossum-dna.html
bornagain77_{November 7, 2012
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