Has The Assumption Of A Unique Genome Been Overthrown

Consensus in the scientific community told us that every cell in our body has a copy of our unique genetic code.  It is an interesting proposal but practically impossible to verify with current technology until now. There has been advances in sequencing technology taking place which make it possible to check this assumption.

Researchers studying induced pluripotent stem cells (iPSC’s) (adult stem cells reprogrammed back to embyro stem cells used for medical treatments) have discovered copy number variations (CNV) in cells derived from skin cells. Most assumed these changes occurred in the process of inducing them to the pluripotent state but Yale researchers checking to see whether CNV’s are also found in the somatic cells from which the iPSC’s were derived.

Their paper published in nature says…

“Using PCR and digital droplet PCR, we show that at least 50% of those CNVs are present as low-frequency somatic genomic variants in parental fibroblasts (that is, the fibroblasts from which each corresponding human iPSC line is derived), and are manifested in iPSC lines owing to their clonal origin. Hence, reprogramming does not necessarily lead to de novo CNVs in iPSCs, because most of the line-manifested CNVs reflect somatic mosaicism in the human skin….”

“Overall, we estimate that approximately 30% of the fibroblast cells have somatic CNVs in their genomes, suggesting widespread somatic mosaicism in the human body. Our study paves the way to understanding the fundamental question of the extent to which cells of the human body normally acquire structural alterations in their DNA post-zygotically.” 

What do they mean by “Somatic mosaicism? It’s basically jargon telling you that genomes differ from cell to cell! But not only in copy number variations (CNV’s), but they discovered it in single nucleotide polymorphisms (SNP’s) also. The long held assumption about you having only one genome is thus falsified. This discovery is telling us we have numerous genomes!

How is this going to affect genetics and evolutionary studies? Ever since the Human Genome Project published its epochal map of “the human genome,” there have been maps of other animals including chimps. But from what we know now about genome variations do those maps reflect reality in nature and are these maps depended upon which somatic cell was sequenced?

Geneticists have been aware of variations between individuals of a species which is why various ethic groups have been included in studies but this new discovery is finding significant variation within an individual’s own cells! It is not known at this time on how significant these changes are considering their study was based only on skin cells. But it is quite possible this could be a game changer…

“The prevailing wisdom has been that every cell in the body contains identical DNA. However, a new study of stem cells derived from the skin has found that genetic variations are widespread in the body’s tissues, a finding with profound implications for genetic screening, according to Yale School of Medicine researchers.”

As far as the story of evolution, it has been claimed for years about small differences between human and chimpanzee genomes. What if the percent difference is a function of the source cells used? If there is a difference then that means any conclusions about human-chimp similarities would prove unreliable. Which cells should be averaged? Will the averages converge or diverge, depending on which cells are selected? Philosophers of science can have fun with this one!

Creationists have taken some of the claims about evolutionary similarities and differences based on genetics with a grain of salt and now this belief has been confirmed by this scientific study! This is going to be one of the more interesting areas in science!

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5 thoughts on “Has The Assumption Of A Unique Genome Been Overthrown

  1. As far as the story of evolution, [sic] it has been claimed for years about [sic] small differences between human and chimpanzee genomes. What if the percent difference is a function of the source cells used? If there is a difference then that means any conclusions about human-chimp similarities would prove unreliable.

    Holy hyperbole, Batman! Michael[1] takes a variation of about 3,000 base pairs,[2] and proclaims that maybe we now have reduced the 30,000,000 base-pair difference between human and chimp genomes[3] to the point where the difference is “unreliable.”

    Let’s see: A CNV from a mosaicism is about 0.001% of the difference between chimp and human, our closest living relative. Those numbers are for the larger effect, copy-number variation of entire genes. But many of the mosaicisms are SNPs.[4] For this type of variation, the difference shrinks to about 1 part in 50 million. One doubts that this would significantly degrade the ability to tell chimp and human genomes apart.

    So the proper comment here is: BWAHAHAHAHAHAAAAAHA

    The bad news here is not so much that creationists are as horrible at math as they are at biology. The bad news is that they seem to expect that their readers are too dumb to figure this out.[5]
    ================

    [1] Well, Michael himself didn’t do it. This time, he plagiarized the Dishonesty Institute’s Evolution News and Views. Without any attribution, of course..

    [2] Back-of-the envelope calc for duplicating a gene, i.e., a CNV..

    [3] di9fference is about 2% between chimp and human.

    [4] single-nucleotide polymorphism, a change in only a single base pair.

    [5] Should we believe the story about a creationist who became a scientist, and lowered the average IQ of both groups?

  2. Michael is enamored of magic in biology. He supposes that if any cell in the body is hit by a cosmic ray and thereby alters one codon of a gene, that every cell in the entire body will magically conform itself to the new genome in the one affected cell—so that all cells will again have the same genome.

    A duplication, of course, involves more than a single codon. But duplication can and does happen. For example, when a body cell divides during growth, chromosomes may become mismatched; an unequal crossover may produce a duplication of an entire gene. Or of several genes. Cancer cells are infamous for aneuploidy, in which entire chromosomes may differ from those of the normal body cells. This effect is called “somatic mosaicism.” Sound familiar?

    So what is the big deal about the result reported in the cited Nature paper? Certainly not that the same individual can have genome differences among the cells of its body. The finding is that induced stem cells may have more of these differences than had been thought. (Remember that these “iPS” cells are the adult stem cells that Michael slavers over periodically.) Although the differences from these CNVs and SNPs are much much smaller than inter-species differences,[1] they could possibly affect the functioning of the stem cell. The significance of the paper is thus that these adult stem cells might not be as safe as thought, because their functions may differ from the parent cell in some ways..

    Although the subject of the study was adult stem cells, the authors wonder whether the larger number of mutations are a result of the stem-cell reprogramming process, or do all somatic cells exhibit this larger amount of mosaicism. For that question, further research is needed.[2]

    .

    So this study has nothing to do with the genetic differences among species. Any attempt to make it so stem from such thoroughgoing ignorance that one can only surmise that it is a deliberate lie.

    Creationists have taken some of the claims about evolutionary similarities and differences based on genetics with a grain of salt and now this belief has been confirmed by this scientific study!

    Another attempt to arrogate a scientific result for creationists. The proper response here is “Horse puckey!” Creationist principles have never in two centuries made any confirmed prediction of anything,[3] nor made any scientific discovery, nor contributed in the slightest to any advance for the benefit of man kind.

    ===========

    [1] See my previous comment, above..

    [2] Note that one of the major purposes of publishing scientific papers is to suggest avenues for further research. This is in contrast to creationist papers, whose only purpose is to confirm the faith of the scientifically illiterate.

    [3] Michael I (and the Disco Tute) should remember that a “prediction” can only be made before /i> the confirmatory results are known—afterward doesn’t count.

  3. What if the percent difference is a function of the source cells used? If there is a difference then that means any conclusions about human-chimp similarities would prove unreliable.

    BUT WAIT!! Suppose Michael were correct, and that this discovery makes it more difficult to tell human and chimp genomes apart.

    The genome determines the appearance and functioning of the animal that houses it. If it would be difficult to tell humans apart from chimps genetically, then there would be a number of people walking around that look and act like chimpanzees (and vice versa).

    Now I don’t know any of Michael’s relatives personally, but perhaps he has actually observed that some of them have the long arms, receding brows, and small brains of a chimp.[1]

    But then perhaps Michael wouldn’t notice.

    ===================

    [1] Don’t forget, also, that genetic variations among chimps is several times as great as that among humans (of all races), increasing the possibility of overlap. A comprehensive study to this effect was reported in the April 2007 issue of PLoS Genetics

  4. As far as the story of evolution, [sic] it has been claimed for years about [sic] small differences between human and chimpanzee genomes.

    Here’s another small difference, not between genomes, but between human and chimp biomes.

    The microbial communities that inhabit the gut of chimps assort into three enterotypes that are compositionally similar to those that inhabit the human gut.. Each of theses is dominated by the same set of bacterial genera. The results from 35 chimps suggest that this is an ancient trait that was present in the great apes before the divergence of humans and chimps more than 5 million years ago.

    See Moeller, et al., “Chimpanzees and humans harbour compositionally similar gut enterotypes” Nature Communications 3, 1179, pub. 13 Nov. 2012.

  5. THIS JUST IN

    Last Tuesday (Nov 27, 2012) Pat Robertson said on his 700 Club show[1] that the world need not have been created 6,000 years ago. That Old Bishop Ussher might have been wrong. And that dinosaurs lived before humans appeared.

    Robertson was replying to a viewer’s letter complaining that her children were questioning Genesis, and she wanted to know how to get them back on the True Path. At the conclusion of the clip, Robertson said, “If you fight revealed science, you’re going to lose your children.”

    =================

    [1] The clip was posted on Panda’s Thumb, Nov. 29. YouTube link here.

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