“The Unbearable Lightness of Chimp-Human Genome Similarity” by Rick Sternberg

_{Salvador Cordova

May 18, 2009

Darwinism, Intelligent Design}

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Walter ReMine once said to me, the supposed 99.5% identity between chimps and humans is like taking two books, creating an alphabetical listing of all the unique words in each book, and then comparing the lists of unique words derived from each book. It would be really easy then to use these lists to argue: “see the books are 99.5% identical!”

Another ID proponent, David Pogge, argued that the sequence comparison are like comparing driving directions: two sets of directions can have 99% similarity, but a few differences can lead to radically different destinations.

With this in mind, here is Rick Sternberg’s Guy Walks Into a Bar and Thinks He’s a Chimpanzee: The Unbearable Lightness of Chimp-Human Genome Similarity.

Comments

So... the answer is, normal scientists will continue working and as more information about biology comes to light, the more it reinforces ID.eintown_{May 18, 2009
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I assume that if we were to gain higher understanding of the syntax and logic used in the highly specified multi-dimensional genetic code that we see in organisms, including how the code itself could possibly be standardized(Such as the assembly language used in HMIs for example), then we'd be that much closer to a solid conclusion for a design inference. But again we're just now discovering layers of the code that were never even conceivable before, and were initially written off as vestigial junk. Once we truly understand from every angle how the code is integrated within biological systems, then I'm sure we could positively quantify the plausibility of common descent vs. common design. From my own perspective, every single further discovery we make is moving the goalposts closer for common design. I do however feel that the philosophical bias within purely naturalistic thinking is retarding this process, kind of like trying to look for a field of daisies within the heart of a volcano, and shutting out anyone who advises that you won't find them in there.PaulN_{May 18, 2009
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genetic engineering and artificial selection where intelligence is guiding the process How precisely would test for this?eintown_{May 18, 2009
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Sure ID is compatible with common descent, but not exclusively. Obviously another pursuit of high interest would be common design among species that share similarities at the phenotype and genotype level. Of course this pursuit requires a fundamentally different perspective from all of the presuppositions that build the explanatory framework for common descent. The first step in doing so would be to realize that there's more than one way to explain similarities between species, including but not limited to genetic engineering and artificial selection where intelligence is guiding the process. Also quantifying the testable and observable physical/chemical limits to RM+NS and other naturalistic processes would serve to bolster this proposition.PaulN_{May 18, 2009
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sorry about the italics! Also, Nakashima is correct... I thought ID is OK with common descent?eintown_{May 18, 2009
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I don't understand why Dr Sternberg bothers having this conversation in the first place, unless his correspondent is extremely good looking. He could have simply stated that from an ID perspective, no one doubts the common descent of humans and simians, and the details are being worked out. Is he actually trying to argue that the ITSs observed in different species are designed artifacts? That would seem to be a testable prediction.Nakashima_{May 18, 2009
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Which is like comparing words between books, and a lot less like comparing paragraphs and chapters. No, its not. Comparing words is analogous to comparing nucleotides. Comparing ideas in a book is analogous to comparing genes. Also what you were saying about linkage blocks and genome lengths. The position of genes does not have as much affect that the sequence of the genes. Also, the coding parts of the genome are very important for alignment and similarity. Parts of the genome that do not have a function will accumulate random mutations over time, so conserved regions (i.e. coding regions) are more useful, as there is a constraint to changes.eintown_{May 18, 2009
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N.b. that our fused chromosome 2 has similar contents to two of the chimp chromosomes doesn't say a lot when you consider that we are 90 odd percent identical.Green_{May 18, 2009
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A good point that Casey Luskin makes about human chromosome 2 and how it is a fusion of two chimp chrosmomes (2a and 2b) is this: Humans may have begun with 48 chromosomes, and undergone a chromosomal fusion *within* the human lineage. This has happened in mice, and horses. Mice generally have 40 chromosomes, but some populations have undergone a chromosomal fusion and now have 38 chromosomes. Other races of mice have as low as 22. The same goes for different breeds of horses. So our fused chromosome 2 is equally compatible with comon ancestry as it is uncommon ancestry.Green_{May 18, 2009
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For starters, I posted here: Humans only 94% similar to chimps, not 98.5%
Homo Sapein Genome size = 3,4000,00,000 Pan Troglodytes= 3,577,500,000 That is technically a difference of 177,500,000.
3,577,500,000 / 3,400,000,000 -1 = 5.2% That figure is 10 times larger than the supposed 0.5% difference suggested in some literature. And Rick noted:
Also, the 99% identity figure is often derived from protein-coding regions that only comprise about 1.5% of the two genomes.
scordova_{May 18, 2009
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When doing alignments, you can’t really take an entire genome and align it with another. That would require way too much computer power. Instead, the genomes are spliced up and those bits are aligned, which is far less computationally intensive.
Which is like comparing words between books, and a lot less like comparing paragraphs and chapters. However, with intra-species comparison, do we have these same problems with alignment. I would presume we could compare entire chromosomes of linkgage blocks between humans, say hundreds of millions of base pairs at a time versus individual genes (with about 1200 base pairs). Thus comparing between members of the same species (like human to human) is more like being able to compare entire chapters. Is this correct? Thank you again for your comments. We don't have enough biologists at UD, most are engineers like me....scordova_{May 18, 2009
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I don't have extensive experience with complicated alignments. I usually work on simple intra-specie genomes. When doing alignments, you can't really take an entire genome and align it with another. That would require way too much computer power. Instead, the genomes are spliced up and those bits are aligned, which is far less computationally intensive. Generally when comparing genomes, one looks at highly conserved regions. As the regions are highly conserved, there will be little change over time. If there is a lot of change, the 2 organisms are evolutionary distant (i.e. diverged a while ago); a little change, would show a more recent time of divergence.eintown_{May 18, 2009
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Eintown, I understand your specialty is in molecular biology. Can you describe a little bit about sequence alignments. Do we have to do considerable amount of sequence alignment between chimps genomes and human genomes versus comparing two human genomes to each other? Isn't comparing two human genomes more like comparing two versions of the same book? Whereas comparing chimp and human genomes involves quite a bit of realignments, like Walter suggested. Thanks. Salscordova_{May 18, 2009
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Hmm, that is better, but the analogy is not very effective. If I take 2 books about how to play sports - one on soccer and another on rubgy, they will have, 99% alignment. However the outcome - i.e. once the books are read practiced- 2 very different games are played. It's misleading to say that the two books are 99% the same. The structure, maybe, but not the content. Its the same thing with genetic similarity. 99% is very similar, but there are differences.eintown_{May 18, 2009
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Good post, Sal.tribune7_{May 18, 2009
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However nucleotides are not being compared between organisms - rather genes.
Thank you for your comment. I believe Walter was referring to genes as words and nucleotides (or even nucleotide triplets) as letters. So I beleive Walter's analogy is correct. Does that seem reasonable?scordova_{May 18, 2009
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ReMines is not quite correct. The analogy does not fit. He compares the smallest units of meaning (words) between the books. However nucleotides are not being compared between organisms - rather genes. So for his analogy to be correct, one would compare strings of words - or concepts - between the books. Pogge is however correct. Tiny differences - between genes - or directions - can make huge differences.eintown_{May 18, 2009
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You don't mean "unique." If a word is unique to book A, by definition it can't appear in book B, so the similarity would always be zero. "Individual," maybe? Or "distinct?"twvolck_{May 18, 2009
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Ok, how many noticed Rick Sternberg's reference to the music by Piero Umiliani (1969)? Nice bar music eh? :-)scordova_{May 18, 2009
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