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An interesting new paper in human vs. chimp evolution

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Background: Although humans and chimpanzees have accumulated significant differences in a number of phenotypic traits since diverging from a common ancestor about six million years ago, their genomes are more than 98.5% identical at proteincoding loci. This modest degree of nucleotide divergence is not sufficient to explain the extensive phenotypic differences between the two species. It has been hypothesized that the genetic basis of the phenotypic differences lies at the level of gene regulation and is associated with the extensive insertion and deletion (INDEL) variation between the two species. To test the hypothesis that large INDELs (80 to 12,000 bp) may have contributed significantly to differences in gene regulation between the two species, we categorized human-chimpanzee INDEL variation mapping in or around genes and determined whether this variation is significantly correlated with previously determined differences in gene expression.

Results: Extensive, large INDEL variation exists between the human and chimpanzee genomes. This variation is primarily attributable to retrotransposon insertions within the human lineage. There is a significant correlation between differences in gene expression and large human-chimpanzee INDEL variation mapping in genes or in proximity to them.

Conclusions: The results presented herein are consistent with the hypothesis that
large INDELs, particularly those associated with retrotransposons, have played a significant role in human-chimpanzee regulatory evolution.

Of related interest:
The Blind Men and the Ape Man - October 2011 Excerpt: “We have all seen the canonical parade of apes, each one becoming more human. We know that, as a depiction of evolution, this line-up is tosh (nonsense). Yet we cling to it. Ideas of what human evolution ought to have been like still colour our debates.” So said Henry Gee, editor of Nature this month (478, 6 October 2011, page 34, doi:10.1038/478034a), http://crev.info/content/111025-blind_men_and_the_ape_man
And to provide even broader context as to how Darwinists always twist evidence to fit their preconceived conclusion: Why does the genetic similarity, in this following study, not count for establishing a direct line of common descent?
Kangaroo genes close to humans Excerpt: Australia's kangaroos are genetically similar to humans,,, "There are a few differences, we have a few more of this, a few less of that, but they are the same genes and a lot of them are in the same order," ,,,"We thought they'd be completely scrambled, but they're not. There is great chunks of the human genome which is sitting right there in the kangaroo genome," http://www.reuters.com/article/science%20News/idUSTRE4AH1P020081118
i.e. why do genetic similarity studies only count when Darwinists say they do, and why do genetic dissimilarity studies only count when Darwinists say they do? Assuming the conclusion you preconceived beforehand, no matter what the evidence says afterwards, IS NOT science!!! For atheistic neo-Darwinists to be 'scientific', Darwinists must first prove that mutations to DNA can generate novel body-plan morphogenesis in the first place before they are allowed such unfettered leeway of extrapolation in their genetic similarity/dissimilarity studies as they are now exercising!!! Despite what neo-Darwinists might think, Design is a live option in these studies! Notes:
Response to John Wise - October 2010 Excerpt: But there are solid empirical grounds for arguing that changes in DNA alone cannot produce new organs or body plans. A technique called "saturation mutagenesis"1,2 has been used to produce every possible developmental mutation in fruit flies (Drosophila melanogaster),3,4,5 roundworms (Caenorhabditis elegans),6,7 and zebrafish (Danio rerio),8,9,10 and the same technique is now being applied to mice (Mus musculus).11,12 None of the evidence from these and numerous other studies of developmental mutations supports the neo-Darwinian dogma that DNA mutations can lead to new organs or body plans--because none of the observed developmental mutations benefit the organism. http://www.evolutionnews.org/2010/10/response_to_john_wise038811.html “Yet by the late 1980s it was becoming obvious to most genetic researchers, including myself, since my own main research interest in the ‘80s and ‘90s was human genetics, that the heroic effort to find the information specifying life’s order in the genes had failed. There was no longer the slightest justification for believing that there exists anything in the genome remotely resembling a program capable of specifying in detail all the complex order of the phenotype (Body Plan)." Michael John Denton page 172 of Uncommon Dissent Stephen Meyer - Functional Proteins And Information For Body Plans - video http://www.metacafe.com/watch/4050681 Dr. Stephen Meyer comments at the end of the preceding video,,, ‘Now one more problem as far as the generation of information. It turns out that you don’t only need information to build genes and proteins, it turns out to build Body-Plans you need higher levels of information; Higher order assembly instructions. DNA codes for the building of proteins, but proteins must be arranged into distinctive circuitry to form distinctive cell types. Cell types have to be arranged into tissues. Tissues have to be arranged into organs. Organs and tissues must be specifically arranged to generate whole new Body-Plans, distinctive arrangements of those body parts. We now know that DNA alone is not responsible for those higher orders of organization. DNA codes for proteins, but by itself it does insure that proteins, cell types, tissues, organs, will all be arranged in the body. And what that means is that the Body-Plan morphogenesis, as it is called, depends upon information that is not encoded on DNA. Which means you can mutate DNA indefinitely. 80 million years, 100 million years, til the cows come home. It doesn’t matter, because in the best case you are just going to find a new protein some place out there in that vast combinatorial sequence space. You are not, by mutating DNA alone, going to generate higher order structures that are necessary to building a body plan. So what we can conclude from that is that the neo-Darwinian mechanism is grossly inadequate to explain the origin of information necessary to build new genes and proteins, and it is also grossly inadequate to explain the origination of novel biological form.’ - Stephen Meyer - (excerpt taken from Meyer/Sternberg vs. Shermer/Prothero debate - 2009) Life, Purpose, Mind: Where the Machine Metaphor Fails - Ann Gauger - June 2011 Excerpt: I'm a working biologist, on bacterial regulation (transcription and translation and protein stability) through signalling molecules, ,,, I can confirm the following points as realities: we lack adequate conceptual categories for what we are seeing in the biological world; with many additional genomes sequenced annually, we have much more data than we know what to do with (and making sense of it has become the current challenge); cells are staggeringly chock full of sophisticated technologies, which are exquisitely integrated; life is not dominated by a single technology, but rather a composite of many; and yet life is more than the sum of its parts; in our work, we biologists use words that imply intentionality, functionality, strategy, and design in biology--we simply cannot avoid them. Furthermore, I suggest that to maintain that all of biology is solely a product of selection and genetic decay and time requires a metaphysical conviction that isn't troubled by the evidence. Alternatively, it could be the view of someone who is unfamiliar with the evidence, for one reason or another. But for those who will consider the evidence that is so obvious throughout biology, I suggest it's high time we moved on. - Matthew http://www.evolutionnews.org/2011/06/life_purpose_mind_where_the_ma046991.html#comment-8858161
PaV: "This is the problem with Darwinism: it’s always subject to revision, and never subject to falsification." ==== In other words their present explanations delve deep into the realm of direction, guidance, purpose and goals when it comes to present excuses when finally backed into a corner they have to admit their former position on the matter was extremely flawed even though they viciously defended that position and labled IDists anti-science, dumb, stupid, delusional and any number of assorted insults, vulgarities and personal attacks when all you were doing was truly logically looking at the evidence in the first place. In actuality, they have been proven themselves over and over again to be the ones who had the faith based position on their worldview biased belief in Junk-DNA which they dogmatically defended for some decades. ---- PaV: "The fact that, based on Darwinian assumptions, non-coding DNA was considered “junk”, should be sufficient reason enough to consider it as wrong. Are you willing to do that? Or, is the answer always: “Well, we know Darwinian theory is true; so how shall we change the theory, or change the results, so that it will all conform to the theory?” This line of reasoning is not science, but orthodoxy." ==== Truthfully, all they ever had to do was admit that they didn't know the function of thenoncoding DNA and state simply that they were going to keep researching until they found out what it's function(purpose) is. And that would have been acceptable. But Oh No! The Junk-DNA doctrine fit in quite well with into their religious imaginations of vestigial evolutionary antique collection hold overs. Yet when you point these past gross failings out to them, they play possom and pull a historical revisionist stunt of what they actually meant way back when. Fortunately we have in print what they historically said and insisted and it doesn't jive with the excuses being pimped now. Clearly it's the Theory itself that is the only truly evolving animal. Eocene
perhaps full context???
Darwinian Logic: The Latest on Chimp and Human DNA – Jonathan Wells - October 2011 Excerpt: Protein-coding regions of DNA in chimps and humans are remarkably similar -- 98%, by many estimates -- and this similarity has been used as evidence that the two species are descended from a common ancestor. Yet chimps and humans are very different anatomically and behaviorally, and even thirty years ago some biologists were speculating that those differences might be due to non-protein-coding regions, which make up about 98% of chimp and human DNA. (In other words, the 98% similarity refers to only 2% of the genome.) Now a research team headed by John F. McDonald at Georgia Tech has published evidence that large segments of non-protein-coding DNA differ significantly between chimps and humans,,,, If the striking similarities in protein-coding DNA point to the common ancestry of chimps and humans, why don’t dissimilarities in the much more abundant non-protein-coding DNA point to their separate origins? http://www.evolutionnews.org/2011/10/the_latest_on_chimp_and_human052291.html
further note from article:
These findings add to growing evidence that non-protein-coding regions that some Darwinists have labeled "junk DNA" are not junk after all. But the findings also point to a much more serious problem with Darwinian reasoning. If the striking similarities in protein-coding DNA point to the common ancestry of chimps and humans, why don't dissimilarities in the much more abundant non-protein-coding DNA point to their separate origins? That's because questioning the common ancestry of chimps and humans is taboo. So we're left with the following argument: The (protein-coding) DNA of chimps and humans is similar. Therefore, the two species share a common ancestor. The (non-protein-coding DNA) of chimps and humans is NOT similar. Therefore, the two species share a common ancestor and the dissimilarity explains their differences. Where have we encountered this form of reasoning before? How about vertebrate embryology: The early stages of vertebrate embryos are similar. Therefore, vertebrates share a common ancestor. The early stages of vertebrate embryos are NOT similar. Therefore, vertebrates share a common ancestor but their early stages evolve easily. Apparently, Darwinian "logic" operates this way: Common ancestry is true. X and Y are similar. X and Y are NOT similar. Therefore, common ancestry is true. This is a classical circular argument. Picture an Ouroboros, the alchemical symbol of a snake with its own tail in its mouth (above). Or maybe the never-ending Penrose stairs: (optical illusion of ascending staircase?) Do you get the feeling that Darwinian "logic" is taking us nowhere?
You might start with the fact that there are about 3 million total TE insertions in common between the 2 species. The species specific insertions (most of which are dimorphic) represent less than 1% of the total. PNG
Darwinian Logic: The Latest on Chimp and Human DNA - Jonathan Wells October 27, 2011 Excerpt: If the striking similarities in protein-coding DNA point to the common ancestry of chimps and humans, why don't dissimilarities in the much more abundant non-protein-coding DNA point to their separate origins? http://www.evolutionnews.org/2011/10/the_latest_on_chimp_and_human052291.html bornagain77
Elizabeth: In science all conclusions are provisional. That’s why models and estimates are always subject to revision. This is the problem with Darwinism: it's always subject to revision, and never subject to falsification. The fact that, based on Darwinian assumptions, non-coding DNA was considered "junk", should be sufficient reason enough to consider it as wrong. Are you willing to do that? Or, is the answer always: "Well, we know Darwinian theory is true; so how shall we change the theory, or change the results, so that it will all conform to the theory?" This line of reasoning is not science, but orthodoxy. After reading Behe's "Edge of Evolution", and considering so many other investigations showing the limited capacity of Darwinian mechanisms to change phylogeny, everyone should be asking: "Where did we go wrong in accepting Darwinism whole-hog?" But, then again, I am an "optimist". ;) PaV
Elizabeth: It’s when they don’t revise their models and estimates in the light of new data that they need to apologise. Ditto! :) gpuccio
Why are you owed an apology, PaV? In science all conclusions are provisional. That's why models and estimates are always subject to revision. It's when they don't revise their models and estimates in the light of new data that they need to apologise. Elizabeth Liddle
a few notes as to just how 'constraining' this finding of 'large INDEL variation between the human and chimpanzee genomes' is to the (already falsified) neo-Darwinian model(The Modern Synthesis): ,,, It is worth remembering the alternative splicing code that was deciphered a recent while back:
Canadian Team Develops Alternative Splicing Code from Mouse Tissue Data Excerpt: “Our method takes as an input a collection of exons and surrounding intron sequences and data profiling how those exons are spliced in different tissues,” Frey and his co-authors wrote. “The method assembles a code that can predict how a transcript will be spliced in different tissues.” http://www.genomeweb.com/informatics/canadian-team-develops-alternative-splicing-code-mouse-tissue-data
Indeed, it is also interesting to point out just how extreme the effort was to find the correct algorithm that could find the unique regulatory splicing codes that are unique for each species:
Researchers Crack 'Splicing Code,' Solve a Mystery Underlying Biological Complexity - May 2010 Excerpt: "Understanding a complex biological system is like understanding a complex electronic circuit. Our team 'reverse-engineered' the splicing code using large-scale experimental data generated by the group," http://www.sciencedaily.com/releases/2010/05/100505133252.htm Breakthrough: Second Genetic Code Revealed - May 2010 Excerpt: The paper is a triumph of information science that sounds reminiscent of the days of the World War II codebreakers. Their methods included algebra, geometry, probability theory, vector calculus, information theory, code optimization, and other advanced methods. One thing they had no need of was evolutionary theory,,, http://crev.info/content/breakthrough_second_genetic_code_revealed
But to point out why this 'Extensive, large INDEL variation' is very antagonistic to neo-Darwinism: Finding different regulatory codes regulating the genetic code of different species is, of course, a very constraining thing for the neo-Darwinian genetic reductionism scenario, (Modern Synthesis), to account for, since 'strict' neo-Darwinism holds that all variations must arise from variation to the genetic code itself. Yet another constraint to neo-Darwinism is also found, from this particular line of evidence, by neo-Darwinism's inability to account for increasing complexity of any particular code; Regulatory code, Genetic code, or any other code that may be found in life. This 'other' constraint on neo-Darwinism is called Shannon Channel capacity;
Shannon Information - Channel Capacity - Perry Marshall (Communications Technician) - video http://www.metacafe.com/watch/5457552/ “Because of Shannon channel capacity that previous (first) codon alphabet had to be at least as complex as the current codon alphabet (DNA code), otherwise transferring the information from the simpler alphabet into the current alphabet would have been mathematically impossible” Donald E. Johnson – Bioinformatics: The Information in Life
Further notes:
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/ Ends and Means: More on Meyer and Nelson in BIO-Complexity - September 2011 Excerpt: According to Garrett and Grisham's Biochemistry, the aminoacyl tRNA snythetase is a "second genetic code" because it must discriminate among each of the twenty amino acids and then call out the proper tRNA for that amino acid: "Although the primary genetic code is key to understanding the central dogma of molecular biology on how DNA encodes proteins, the second genetic code is just as crucial to the fidelity of information transfer." http://www.evolutionnews.org/2011/09/ends_and_means050391.html The data compression of some stretches of human DNA is estimated to be up to 12 codes thick (12 different ways of DNA transcription) (Trifonov, 1989). (This is well beyond the complexity of any computer code ever written by man). John Sanford - Genetic Entropy The multiple codes of nucleotide sequences. Trifonov EN. - 1989 Excerpt: Nucleotide sequences carry genetic information of many different kinds, not just instructions for protein synthesis (triplet code). http://www.ncbi.nlm.nih.gov/pubmed/2673451 "In the last ten years, at least 20 different natural information codes were discovered in life, each operating to arbitrary conventions (not determined by law or physicality). Examples include protein address codes [Ber08B], acetylation codes [Kni06], RNA codes [Fai07], metabolic codes [Bru07], cytoskeleton codes [Gim08], histone codes [Jen01], and alternative splicing codes [Bar10]. Donald E. Johnson – Programming of Life – pg.51 - 2010 DNA Caught Rock 'N Rollin': On Rare Occasions DNA Dances Itself Into a Different Shape - January 2011 Excerpt: Because critical interactions between DNA and proteins are thought to be directed by both the sequence of bases and the flexing of the molecule, these excited states represent a whole new level of information contained in the genetic code,
PaV: Where is the apology we are owed? An optimist, if I ever saw one! :) gpuccio
This paper is reported today over at PhysOrg.com. The original article is, of course, more pertinent. However, the headline over at PhysOrg is that it is "junk-DNA" that is responsible for the differences between humans and chimps. You remember: "junk DNA". Stuff that was unimportant, and clearly demonstrated that a "intelligent designer" could not be involved in the evolution of life. Arthur Hunt has been here at UD minimizing the importance of "junkDNA". There are other Darwinian thinkers that have a hard time with junk-DNA. But, all along, IDists, in spite of heavy criticism and scorn, predicted that important functions would be found for so-called "junkDNA". (Meanwhile, Darwinists, in the face of genome-wide studies, had to go from humans having 100,000 genes, to having 30,000 genes, to have a little over 20,000 genes---so in love with, and convinced of the importance of, the role of genes in determining phenotypic change) Where is the apology we are owed? PaV
PNG: I think you make a good point. gpuccio
What I found remarkable about this paper is that it takes no account of dimorphism and allele frequencies of transposon insertions. A lot of recent work has shown that a large portion of species-specific TE insertions in any given human genome are not fixed, that is, the allele frequency is < 1. You can't account for species differences by looking at insertions that have a low frequency. Identifying which insertions are fixed in the population is necessary before you can tell if they are significant for morphological or other differences. But, for those who deny common descent, the first thing to grasp is not the species-specific insertions - it is the 3 million insertions that humans and chimps share at orthologous loci. There are only 2 ways to account for that - common descent or miracles, lots and lots of them. If you can think of another alternative, let me know. PNG
Anyway, I don’t believe in the importance of counting how different we are at genetic level from chimps, and fighting about numbers and percentages. We are different at phenotipic level. Very different. Genetic analysis must explain that. If it can’t, it simply means that our genetic analysis is flawed, or incomplete.
Well I agree to some extent about the counting. Percentages are tricky things, like probabilities (to which they are closely related) and you always have to ask: percentage/probability of what? Phenotypically we different in many ways (and similar also, in many important ways) and what is interesting is what makes us phenotypically different. Some of that is genetic, but not all. Some, at least, is cultural, the most obvious being language. Language capacity is transmitted genetically, but language itself is transmitted culturally, and the referents we have signifiers for, including abstractions like "love" and "justice" and "morality", are almost certainly at least partially culturally transmitted as well. Elizabeth Liddle
Well, me too. As is anyone involved in the development and function of organisms :) Elizabeth Liddle
Elizabeth: Ah, and I am always pleased when I see new accounts of the importance of retrotransposons. As an IDists, I am a great fan of them, and of all non coding DNA. gpuccio
Elizabeth: I agree with the general idea that the most important differences between humans and chimps will be shown at regulatory level, and especially at the level of hidden procedures, that at present still defy our understanding. That is consistent with the lower rate of emergenge of new protein domains in the last phases of evolution. However, I would like to mention that the problem of human orphan genes is a true one. In the past, I examined in detail the paper about those 1000 genes were taken off from the count, and I must say that the methodology was very, very biased. I am not sure those 1000 genes are true genes, but I am rather sure that the reasons why thet were "eliminated" from the list are not good reasons. Anyway, I don't believe in the importance of counting how different we are at genetic level from chimps, and fighting about numbers and percentages. We are different at phenotipic level. Very different. Genetic analysis must explain that. If it can't, it simply means that our genetic analysis is flawed, or incomplete. gpuccio
Could you explain your question more clearly? I'm not seeing your point. Elizabeth Liddle
So according to this evolution (at least macro-evolution) it is not anymore about ramdom point mutations, but ramdom insertion-deletion of retrotransposons. What are we going to do with all that molecular clocks? Blas
What, in your citations, ba77, contradicts the claim that "[chimp and human] genomes are more than 98.5% identical at proteincoding loci"? The claim is not that proteins are 98.5% identical, nor that genes are 98.5% identical, but that the sequences that code for proteins are 98.5% identical. The paper specifically suggests that the important differences may be in non-coding INDELs relevant to the regulation of gene expression. Elizabeth Liddle
Since I'm pretty sure atheists will not correct this mistake, as to this statement:
their genomes are more than 98.5% identical at proteincoding loci.
This statement is WRONG!
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 Chimps are not like humans - May 2004 Excerpt: the International Chimpanzee Chromosome 22 Consortium reports that 83% of chimpanzee chromosome 22 proteins are different from their human counterparts,,, The results reported this week showed that "83% of the genes have changed between the human and the chimpanzee—only 17% are identical—so that means that the impression that comes from the 1.2% [sequence] difference is [misleading]. In the case of protein structures, it has a big effect," Sakaki said. http://cmbi.bjmu.edu.cn/news/0405/119.htm 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
This following article, which has a direct bearing on the 98.8% genetic similarity myth, shows that over 1000 'ORFan' genes, that are completely unique to humans and not found in any other species, and that very well may directly code for proteins, were stripped from the 20,500 gene count of humans simply because the evolutionary scientists could not find corresponding genes in primates. In other words evolution, of humans from primates, was assumed to be true in the first place and then the genetic evidence was directly molded to fit in accord with their unproven assumption. It would be hard to find a more biased and unfair example of practicing science!
Human Gene Count Tumbles Again - 2008 Excerpt: Scientists on the hunt for typical genes — that is, the ones that encode proteins — have traditionally set their sights on so-called open reading frames, which are long stretches of 300 or more nucleotides, or “letters” of DNA, bookended by genetic start and stop signals.,,,, The researchers considered genes to be valid if and only if similar sequences could be found in other mammals – namely, mouse and dog. Applying this technique to nearly 22,000 genes in the Ensembl gene catalog, the analysis revealed 1,177 “orphan” DNA sequences. These orphans looked like proteins because of their open reading frames, but were not found in either the mouse or dog genomes. Although this was strong evidence that the sequences were not true protein-coding genes, it was not quite convincing enough to justify their removal from the human gene catalogs. Two other scenarios could, in fact, explain their absence from other mammalian genomes. For instance, the genes could be unique among primates, new inventions that appeared after the divergence of mouse and dog ancestors from primate ancestors. Alternatively, the genes could have been more ancient creations — present in a common mammalian ancestor — that were lost in mouse and dog lineages yet retained in humans. If either of these possibilities were true, then the orphan genes should appear in other primate genomes, in addition to our own. To explore this, the researchers compared the orphan sequences to the DNA of two primate cousins, chimpanzees and macaques. After careful genomic comparisons, the orphan genes were found to be true to their name — they were absent from both primate genomes. http://www.sciencedaily.com/releases/2008/01/080113161406.htm
The sheer, and blatant, shoddiness of the science of the preceding study should give everyone who reads it severe pause whenever, in the future, someone tells them that genetic studies have proven evolution to be true. If the authors of the preceding study were to have actually tried to see if the over 1000 unique ORFan genes of humans may actually encode for proteins, instead of just written them off because they were not found in other supposedly related species, they would have found that there is ample reason to believe that they may very well encode for biologically important proteins:
A survey of orphan enzyme activities Abstract: We demonstrate that for ~80% of sampled orphans, the absence of sequence data is bona fide. Our analyses further substantiate the notion that many of these (orfan) enzyme activities play biologically important roles. http://www.biomedcentral.com/1471-2105/8/244 Dr. Howard Ochman - Dept. of Biochemistry at the University of Arizona Excerpt of Proposal: The aims of this proposal are to investigate this enigmatic class of genes by elucidating the source and functions of “ORFans”, i.e., sequences within a genome that encode proteins having no homology (and often no structural similarity) to proteins in any other genome. Moreover, the uniqueness of ORFan genes prohibits use of any of homology-based methods that have traditionally been employed to establish gene function.,,, Although it has been hypothesized that ORFans might represent non-coding regions rather than actual genes, we have recently established that the vast majority that ORFans present in the E. coli genome are under selective constraints and encode functional proteins. https://uncommondesc.wpengine.com/intelligent-design/proteins-fold-as-darwin-crumbles/comment-page-5/#comment-358868
Moreover the 'anomaly' of unique ORFan genes is found in every new genome sequenced:
Widespread ORFan Genes Challenge Common Descent – Paul Nelson – video with references http://www.vimeo.com/17135166 Genomes of similar species - Cornelius Hunter PhD. Excerpt: Different variants of the Escherichia coli bacteria, for instance, each have hundreds of unique genes. And some of these genes have been found to have important functions, such as helping to construct proteins. [8] Massive genetic differences were also found between different fruit fly species. The fruit fly is one of the most intensely researched organisms and in recent years a systematic study of the genomes of a dozen different species was undertaken. Evolutionists were surprised to find novel features in the genomes of each of these different fruit fly species. Thousands of genes showed up missing in many of the species, and some genes showed up in only a single species. [9] As one science writer put it, “an astonishing 12 per cent of recently evolved genes in fruit flies appear to have evolved from scratch.” [10] These so-called novel genes would have had to have evolved over a few million years—a time period previously considered to allow only for minor genetic changes. [11,12] ,,, etc.. etc… http://www.darwinspredictions.com/#_4.2_Genomes_of
As alluded to above, completely contrary to evolutionary thought, these 'new' ORFan genes are found to be just as essential as 'old' genes for maintaining life:
Age doesn't matter: New genes are as essential as ancient ones - December 2010 Excerpt: "A new gene is as essential as any other gene; the importance of a gene is independent of its age," said Manyuan Long, PhD, Professor of Ecology & Evolution and senior author of the paper. "New genes are no longer just vinegar, they are now equally likely to be butter and bread. We were shocked." http://www.sciencedaily.com/releases/2010/12/101216142523.htm New genes in Drosophila quickly become essential. - December 2010 Excerpt: The proportion of genes that are essential is similar in every evolutionary age group that we examined. Under constitutive silencing of these young essential genes, lethality was high in the pupal (later) stage and (but was) also found in the larval (early) stages.
their genomes are more than 98.5% identical at proteincoding loci.
Well YEAH! Most proteins are for sustaining the organism and seeing the two organisms are similar I would expect their sustaining proteins to be very similar. Joseph

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