Blame God for cancer …

wd400, I'm sure you can drop him a e-mail and he can much better answer your specific question(s) than I can. As for myself, I'm anticipating Jeffrey Tomkins' further work incorporating lincRNAs and vlincRNAs to further highlight human uniqueness. As well, I look forward to his comparison of 'human protein-coding regions to those in chimpanzees', in which he expects to,,

"provide a much more detailed picture of what makes humans unique and will further demonstrate we are not evolved apes."

I fully expect him to be successful in his endeavor since, in regards to lincRNAs and vlincRNAs,,, microRNA's have already 'torn apart traditional ideas about the animal family tree',,,

Phylogeny: Rewriting evolution - Tiny molecules called microRNAs are tearing apart traditional ideas about the animal family tree. - Elie Dolgin - 27 June 2012 Excerpt: “I've looked at thousands of microRNA genes, and I can't find a single example that would support the traditional tree,” he says. "...they give a totally different tree from what everyone else wants.” (Phylogeny: Rewriting evolution, Nature 486,460–462, 28 June 2012) (molecular palaeobiologist - Kevin Peterson) Mark Springer, (a molecular phylogeneticist working in DNA states),,, “There have to be other explanations,” he says. Peterson and his team are now going back to mammalian genomes to investigate why DNA and microRNAs give such different evolutionary trajectories. “What we know at this stage is that we do have a very serious incongruence,” says Davide Pisani, a phylogeneticist at the National University of Ireland in Maynooth, who is collaborating on the project. “It looks like either the mammal microRNAs evolved in a totally different way or the traditional topology is wrong. http://www.nature.com/news/phylogeny-rewriting-evolution-1.10885

And this 'tearing apart' includes the hypothetical chimp-human connection:

Gene Regulation Differences Between Humans, Chimpanzees Very Complex – Oct. 17, 2013 Excerpt: Although humans and chimpanzees share,, similar genomes (70% per Tomkins), previous studies have shown that the species evolved major differences in mRNA expression levels.,,, http://www.sciencedaily.com/releases/2013/10/131017144632.htm

Thus in regards to lincRNAs and vlincRNAs I expect Darwinists to be surprised yet again by Thomkins' work. Of related note: Finding microRNA's to be severely discordant with Darwinian expectations, as well as finding genetic regulatory networks, and alternative splicing patterns in general, to be unique to both chimps and humans, of which RNA's are a major part, will be extremely problematic for Darwinists (understatement) since ENCODE has already called for a redefinition of the concept of a gene (not that that will stop people like you, wd400, from pretending the 'gene' still does matter):

Landscape of transcription in human cells – Sept. 6, 2012 Excerpt: Here we report evidence that three-quarters of the human genome is capable of being transcribed, as well as observations about the range and levels of expression, localization, processing fates, regulatory regions and modifications of almost all currently annotated and thousands of previously unannotated RNAs. These observations, taken together, prompt a redefinition of the concept of a gene.,,, Isoform expression by a gene does not follow a minimalistic expression strategy, resulting in a tendency for genes to express many isoforms simultaneously, with a plateau at about 10–12 expressed isoforms per gene per cell line. http://www.nature.com/nature/journal/v489/n7414/full/nature11233.html Time to Redefine the Concept of a Gene? - Sept. 10, 2012 Excerpt: As detailed in my second post on alternative splicing, there is one human gene that codes for 576 different proteins, and there is one fruit fly gene that codes for 38,016 different proteins! While the fact that a single gene can code for so many proteins is truly astounding, we didn’t really know how prevalent alternative splicing is. Are there only a few genes that participate in it, or do most genes engage in it? The ENCODE data presented in reference 2 indicates that at least 75% of all genes participate in alternative splicing. They also indicate that the number of different proteins each gene makes varies significantly, with most genes producing somewhere between 2 and 25. Based on these results, it seems clear that the RNA transcripts are the real carriers of genetic information. This is why some members of the ENCODE team are arguing that an RNA transcript, not a gene, should be considered the fundamental unit of inheritance. http://networkedblogs.com/BYdo8 The Extreme Complexity Of Genes – Dr. Raymond G. Bohlin – video http://www.metacafe.com/watch/8593991/

Moreover, in regards to protein coding regions (i.e. Genes), the supposed '99%' pride and joy of Darwinian dogmatists, the fact of the matter is that I fully expect Tomkins to blow a major whole in that myth as well since, as I'm sure you are well aware, a surprising, and extremely large percentage of ORFan genes have recently caught Darwinists by complete surprise:

Genes from nowhere: Orphans with a surprising story - 16 January 2013 - Helen Pilcher Excerpt: When biologists began sequencing genomes they discovered up to a third of genes in each species seemed to have no parents or family of any kind. Nevertheless, some of these "orphan genes" are high achievers (are just as essential as 'old' genes),,, http://ccsb.dfci.harvard.edu/web/export/sites/default/ccsb/publications/papers/2013/All_alone_-_Helen_Pilcher_New_Scientist_Jan_2013.pdf Orphan Genes (And the peer reviewed 'non-answer' from Darwinists) - video http://www.youtube.com/watch?v=1Zz6vio_LhY

Throw on top of all that that Darwinists cannot even explain the fixation of one or two mutations during the hypothesized timescale, then perhaps wd400 you can begin to see the reason why I have such optimism in Tomkin's coming work in the following year or so.

More from Ann Gauger on why humans didn’t happen the way Darwin said - July 2012 Excerpt: Facing Facts But six million years is the entire time allotted for the transition from our last common ancestor with chimps to us according to the standard evolutionary timescale. Two hundred and sixteen million years takes us back to the Triassic, when the very first mammals appeared. One or two mutations simply aren’t sufficient to produce the necessary changes— sixteen anatomical features—in the time available. At most, a new binding site might affect the regulation of one or two genes. https://uncommondesc.wpengine.com/intelligent-design/more-from-ann-gauger-on-why-humans-didnt-happen-the-way-darwin-said/

Verse and Music:

John 1:3-4 All things were made through Him, and without Him nothing was made that was made. In Him was life, and the life was the light of men. Natalie Grant - Your Great Name - live https://www.youtube.com/watch?v=JRREa_pQFcs

bornagain77

BA, I don't suppose you can tell my why Tompkins thinks "According to evolutionary reasoning, the chromosomal areas between humans and chimps that were the most different should have had high levels of genetic recombination" I don't know any reason to imagine this, and can think of two reasons to think it's likely to be wrong (some variants repress recombination, and recombination repression during the early stages of speciation might favour more rapid divergence). wd400

BA77, Thanks for the "Guy walks into a bar" (Sternberg) link @ 13. As WD400 indicated, the chimp issue is not directly relevant to the OP article about Neanderthals. But at least the chimp DNA used is fresh whereas the Neanderthal DNA is thousands of years old, which creates additional obstacles for direct comparison. Piltdown2

Genetic Recombination Study Defies Human-Chimp Evolution by Jeffrey Tomkins, Ph.D. * - May 31, 2013 Excerpt: A recent study, published in the journal Molecular Biology and Evolution, evaluated various regions of the chimpanzee and human genomes for genetic recombination frequency by determining the DNA variability (differences) within large populations of both humans and chimpanzees.1 The researchers found that genetic recombination levels were much higher in regions of the genome between humans and chimps where sequence identity was higher. In the regions of much lower DNA similarity, which occur as differences in gene order, gene content, and other major DNA sequence differences—the recombination rates were much lower.,, These results are the exact opposite of what evolutionists expected. According to evolutionary reasoning, the chromosomal areas between humans and chimps that were the most different should have had high levels of genetic recombination that would help explain why they were so different. But these chromosomal areas that were the most different between humans and chimpanzees had the lowest levels! More recombination equals more evolutionary differences right? Apparently not! Once again, new scientific data has falsified a prominent evolutionary hypothesis. While this study failed to uphold the hypothetical predictions of evolution, it did vindicate the now well-established fact that genetic recombination is a highly regulated, and complex bio-engineered feature that helps create variability in just the right areas of the genome. Other recent research has shown that the human and chimpanzee genomes are radically different(70% indentity).5 And now this new study has demonstrated that these differences are not due to a mythical evolutionary tinkering and shuffling process associated with genetic recombination, but because humans and chimps were created separately and uniquely. http://www.icr.org/article/7526/ Groundbreaking Genetic Discoveries Challenge Ape to Human Evolutionary Theory – June 17, 2013 Excerpt: Ultimately, the study results were contradictory to what evolutionists had theorized. Not only were genetic recombination rates markedly low in areas of human-chimp DNA differences (“rearranged” chromosomes), but the rates were much higher in areas of genetic similarity (“collinear” chromosomes). This is the reverse of what evolutionists had predicted. “The analysis of the most recent human and chimpanzee recombination maps inferred from genome-wide single-nucleotide polymorphism data,” the scientists explained, “revealed that the standardized recombination rate was significantly lower in rearranged than in collinear chromosomes.” Jeffrey Tomkins, a Ph.D. geneticist with the Institute for Creation Research (ICR), told the Christian News Network that these results were “totally backwards” from what evolutionists had predicted, since genetic recombination is “not occurring where it’s supposed to” under current evolutionary theory. Dr. Tomkins further emphasized that evolutionists greatly exaggerate the genetic similarities between humans and chimps, and often ignore areas of DNA where major differences do exist. “It’s called cherry-picking the data,” he explained. “There are many genetic regions between humans and chimps that are radically different. In fact, humans have many sections of DNA that are missing in chimps and vice versa. Recent research is now showing that the genomes are only 70% similar overall.”,,, http://christiannews.net/2013/06/17/groundbreaking-genetic-discoveries-challenge-ape-to-human-evolutionary-theory/ bornagain77

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 bornagain77

Yes the controversy is taking the similarity and decalring it evidence for common ancestry. Joe

Piltdown, There is no controversy around the similarity between the human and chimp genomes, at least among people who know a little genetics. You can browse the human genome with the percentage idenity to chimp if you like: http://ecrbrowser.dcode.org/xB.php?db=hg19&location=chr14:57264985-57279624 There are, of course, regions of the genome that get greater or fewer mutations, but that's not relevant to the neanderthal studies since these variants are spread across the entire genome. wd400

Sorry, last 'graph should say If we assume most of the variants are selectively neutral, then they should follow a similar distribution as the entire genome. In other words, the base-pair sequence of your genome is ~99% identical to a chimp, but (if you have no recent African descent) ~4% of those bases passed through a neanderthal body on their way to you. (If it helps, this is the same way you have ~50% of your mother's genes while being much more than 99.9% similar at a sequence level) wd400

wd400, As BA77's posts indicate, there is significant controversy about the percentage of similarity between genomes. Also, while portions of the genome are extremely resistant to mutation, other portions tolerate (or maybe even encourage) much higher amounts of variation. So I would hesitate to assume an analysis of just one portion of the genome could be extrapolated across the entire genome. Piltdown2

Poltdown, The two numbers are slightly different. If you take a stretch of the human genome and compare it the corresponding sequence in a chimp genome you'll find ~99% of the bases are identical (i.e. "A" in human will almost always correspond with an "A" in chimp). FWIW, if you the same thing among modern humans you'd et 99.9% and human-neanderthal would give 99.7% or so. The recent "admixture" studies have looked only at the variant bases and found that, for people without recent African ancestory, about 4% of the variants are best explained as having entered modern human population by interbreeding. If we assume most of the variants are selective neutral, then they should follow a similar distribution as the entire genome. In other words, you genome has ~99% indentity, but (if you are no of recent African descent) ~4% of the bases in your genome passed through a neanderthal body on their way to you. wd400

Semi Related; Is There "Plenty of Time" (in Texas) for the Evolution of Novelty? - Casey Luskin January 27, 2014 Excerpt: In 2010, Douglas Axe published evidence indicating that despite high mutation rates and generous assumptions favoring a Darwinian process, molecular adaptations requiring more than six mutations before yielding any advantage would be extremely unlikely to arise in the history of the Earth. The following year, Axe published research with developmental biologist Ann Gauger describing the results of their experiments seeking to convert one bacterial enzyme into another closely related enzyme. That is the kind of conversion that evolutionists claim can easily happen. For this case they found that the conversion would require a minimum of at least seven simultaneous changes,15 exceeding the six-mutation-limit that Axe had previously established as a boundary of what Darwinian evolution is likely to accomplish in bacteria. Because this conversion is thought to be relatively simple, it suggests that the model of evolution by gene duplication could not produce even many modest gene conversions. In other experiments led by Gauger and biologist Ralph Seelke of the University of Wisconsin, Superior, their research team broke a gene in the bacterium E. coli required for synthesizing the amino acid tryptophan. When the bacteria's genome was broken in just one place, random mutations were capable of "fixing" the gene. But even when only two mutations were required to restore function, Darwinian evolution got stuck, apparently unable to restore full function.16 This is because it was more advantageous to delete a gene with low functionality or none than it was to continue to express it. This suggests that it is highly unlikely that the standard gene duplication model would produce new complex functions because gene duplicates are likely to be deleted before evolving some new function. - See more at: http://www.evolutionnews.org/2014/01/is_there_plenty081531.html#sthash.VDWizjhg.dpuf bornagain77

Evolution by Splicing - Comparing gene transcripts from different species reveals surprising splicing diversity. - Ruth Williams - December 20, 2012 Excerpt: A major question in vertebrate evolutionary biology is “how do physical and behavioral differences arise if we have a very similar set of genes to that of the mouse, chicken, or frog?”,,, A commonly discussed mechanism was variable levels of gene expression, but both Blencowe and Chris Burge,,, found that gene expression is relatively conserved among species. On the other hand, the papers show that most alternative splicing events differ widely between even closely related species. “The alternative splicing patterns are very different even between humans and chimpanzees,” said Blencowe.,,, http://www.the-scientist.com/?articles.view%2FarticleNo%2F33782%2Ftitle%2FEvolution-by-Splicing%2F A Listener's Guide to the Meyer-Marshall Debate: Focus on the Origin of Information Question -Casey Luskin - December 4, 2013 Excerpt: "There is always an observable consequence if a dGRN (developmental gene regulatory network) subcircuit is interrupted. Since these consequences are always catastrophically bad, flexibility is minimal, and since the subcircuits are all interconnected, the whole network partakes of the quality that there is only one way for things to work. And indeed the embryos of each species develop in only one way." - Eric Davidson http://www.evolutionnews.org/2013/12/a_listeners_gui079811.html Gene Regulatory Networks in Embryos Depend on Pre-existing Spatial Coordinates – Jonathan Wells – July 2011 Excerpt: The development of metazoan embryos requires the precise spatial deployment of specific cellular functions. This deployment depends on gene regulatory networks (GRNs), which operate downstream of initial spatial inputs (E. H. Davidson, Nature 468 [2010]: 911). Those initial inputs depend, in turn, on pre-existing spatial coordinate systems. In Drosophila oocytes, for example, spatial localization of the earliest-acting elements of the maternal GRN depends on the prior establishment of an anteroposterior body axis by antecedent asymmetries in the ovary. Those asymmetries appear to depend on cytoskeletal and membrane patterns rather than on DNA sequences,,, http://www.discovery.org/scripts/viewDB/filesDB-download.php?command=download&id=7751 Gene Regulation Differences Between Humans, Chimpanzees Very Complex – Oct. 17, 2013 Excerpt: Although humans and chimpanzees share,, similar genomes (70% per Tomkins), previous studies have shown that the species evolved major differences in mRNA expression levels.,,, http://www.sciencedaily.com/releases/2013/10/131017144632.htm Darwin or Design? - Paul Nelson at Saddleback Church - Nov. 2012 - ontogenetic depth (excellent update) - video Text from one of the Saddleback slides: 1. Animal body plans are built in each generation by a stepwise process, from the fertilized egg to the many cells of the adult. The earliest stages in this process determine what follows. 2. Thus, to change -- that is, to evolve -- any body plan, mutations expressed early in development must occur, be viable, and be stably transmitted to offspring. 3. But such early-acting mutations of global effect are those least likely to be tolerated by the embryo. Losses of structures are the only exception to this otherwise universal generalization about animal development and evolution. Many species will tolerate phenotypic losses if their local (environmental) circumstances are favorable. Hence island or cave fauna often lose (for instance) wings or eyes. http://www.saddleback.com/mc/m/7ece8/ 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/ A Piece from the Developmental Symphony - February 2012 Excerpt: Embryonic development is an astounding process that seems to happen "automatically.",,, The timing of each step is too precise and the complexity is too intricate to assume that these processes are the mere accumulation by happenstance of changes to regulatory genes. Each gene plays its role at a certain time, and like a symphony, each is activated and silenced in turn such that the final result is a grand performance of orchestrated effort that could only have occurred through design. http://www.evolutionnews.org/2012/02/a_piece_from_th055921.html bornagain77

Using ENCODE Data for Human-Chimp DNA Comparisons by Jeffrey Tomkins, Ph.D.* Excerpt: In 2013, I published a research paper in which chimpanzee chromosomes were sequentially sliced into different sets of small pieces so that the algorithm could optimally compare them to human chromosomes. In so doing, I found that the chimpanzee genome was only about 70 percent similar to the human genome overall.7 More research is needed to show specifically how the new wealth of publicly available ENCODE data can be used beyond basic studies of human-chimp DNA similarity—incorporating lincRNAs and vlincRNAs to further highlight human uniqueness. Research using three large datasets produced by the ENCODE project is now underway at ICR for the purpose of addressing these questions. In a concurrent study, I am also comparing human protein-coding regions to those in chimpanzees. In combination, these new analyses will provide a much more detailed picture of what makes humans unique and will further demonstrate we are not evolved apes. http://www.icr.org/article/7856/ Human Origins(?) by Brian Thomas, M.S. - December 20, 2013 Excerpt: Three major pillars supporting a human-chimp link crashed in 2013. 1. Genetic similarity (70% instead of 98%) 2. beta-globin pseudogene (functional instead of leftover junk) 3. Chromosome 2 fusion site (encodes a functional feature within an important gene instead of a being a fusion site) All three key genetic pillars of human evolution (for Darwinists) turned out to be specious—overstatements based on ignorance of genetic function. http://www.icr.org/article/7867/ "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 (and inquisition style suppression of dissent from Darwinism). Mechanisms and dynamics of orphan gene emergence in insect genomes - January 2013 Excerpt: Orphans are an enigmatic portion of the genome since their origin and function are mostly unknown and they typically make up 10 to 30% of all genes in a genome. http://gbe.oxfordjournals.org/content/early/2013/01/24/gbe.evt009.full.pdf+html Ten years on, still much to be learned from human genome map - April 12, 2013 Excerpt:,,,"What's more, about 10 percent of the human genome still hasn't been sequenced and can't be sequenced by existing technology, Green added. "There are parts of the genome we didn't know existed back when the genome was completed," he said.,,, http://medicalxpress.com/news/2013-04-ten-years-human-genome.html A False Trichotomy Excerpt: The common chimp (Pan troglodytes) and human Y chromosomes are “horrendously different from each other”, says David Page,,, “It looks like there’s been a dramatic renovation or reinvention of the Y chromosome in the chimpanzee and human lineages.” https://uncommondesc.wpengine.com/intelligent-design/a-false-trichotomy/ The evolutionary scientists of the preceding paper offered some evolutionary 'just so' stories of 'dramatically sped up evolution' for why there are such significant differences in the Y chromosomes of chimps and humans, yet when the Y chromosome is looked at for its rate of change we find there is hardly any evidence for any change at all, much less the massive changes the evolutionists are required to explain. Theory of the 'Rotting' Y Chromosome Dealt a Fatal Blow - February 2012 Excerpt: "the sequence of the rhesus Y, shows the chromosome hasn't lost a single ancestral gene in the past 25 million years. By comparison, the human Y has lost just one ancestral gene in that period, and that loss occurred in a segment that comprises just 3% of the entire chromosome", ",,,earlier work comparing the human and chimpanzee Ys revealed a stable human Y for at least six million years. "Now our empirical data fly in the face of the other theories out there. With no loss of genes on the rhesus Y and one gene lost on the human Y, it's clear the Y isn't going anywhere." http://www.sciencedaily.com/releases/2012/02/120222154359.htm bornagain77

Pretty much this is my point. Percentage of similarity is whole lot more complicated than the article implies. Leaves you with the impression that long strings of characters have been lined up side by side and that they are simply reporting the percentage of characters that line up. It's actually a whole lot more complicated, and usually only a small portion of the genome is actually being compared. Also of interest in the article is the implication of the interbreeding of modern humans with Neanderthals. Interbreeding suggests they should not be considered separate species. Piltdown2

How are the %'s calculated? From what I've read, it seems that once we delve into the calculations we find some pretty strange and generous assumptions about what "similar" means. Eric Anderson

I think the approximation for chimpanzee DNA is 98.8% similar to modern humans, and the range of neanderthal DNA is 1-4% in non-African modern humans varied by region (for example 2% Europe, and 1.5% Asia). So its not exactly like we are 98% chimp and 2% neanderthal, since Neanderthal would also been similar to Chimpanzee the overlaps would have necessarily occurred. I literally have no idea sure what percentage neanderthal DNA separated or united us to the chimpanzee. However from what I read, we have altered an addition 8% since this intermingling from the Chimps. Which suggests that we have only separated an about 0.001% from the Chimpanzee since the intermingling. Doktillia

So this article pegs our DNA as 2% neanderthal, and previous articles said it's 98% chimpanzee. Doesn't leave a whole lot of room for anything else. Or maybe these percentages don't mean much. Piltdown2