Horizontal gene transfer: The world is just a DNA scrap yard

_{Denyse O'Leary

July 28, 2014

Darwinism, horizontal gene transfer, News

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Darwinism
horizontal gene transfer
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Click to enlarge — Bacteria incorporating DNA fragments/Katrine Harving Holm

And bacteria are the Class A mechanics loading up on spare parts.

From ScienceDaily:

Our surroundings contain large amounts of strongly fragmented and damaged DNA, which is being degraded. Some of it may be thousands of years old. Laboratory experiments with microbes and various kinds of DNA have shown that bacteria take up very short and damaged DNA from the environment and passively integrate it in their own genome. Furthermore this mechanism has also been shown to work with a modern bacteria’s uptake of 43,000 years old mammoth DNA. The results are published now in the scientific journal Proceedings of the National Academy of Sciences (PNAS). The discovery of this second-hand use of old or fragmented DNA may have major future consequences.

Particularly for hospitals, perhaps.

Postdoc Søren Overballe-Petersen from the Centre for GeoGenetics at the Natural History Museum of Denmark is first author on the paper and he says about the findings: “It is well-known that bacteria can take up long intact pieces of DNA but so far the assumption has been that short DNA fragments were biologically inactive. Now we have shown that this assumption was wrong. As long as you have just a tiny amount of DNA left over there is a possibility that bacteria can re-use the DNA. One consequence of this is in hospitals that have persistent problems with antibiotic resistance. In some cases they will have to start considering how to eliminate DNA remnants. So far focus has been on killing living pathogen bacteria but this is no longer enough in the cases where other bacteria afterwards can use the DNA fragments which contain the antibiotic resistance.”

Her’s the Abstract: (paywall)

Note that for any life form that can so easily engage in horizontal gene transfer, phylogenies based on Darwinian evolution (natural selection acting on random mutation) are now doubtful.

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Hat tip: Timothy Kershner

Comments

Acartia_bogart I don't see how increasing the size of a pool of what you should find as neccessarily random mutations as helpful for Darwin.
The ID argument has always been that random mutations couldn’t account for the variation that we see (again, not true). But now we see that populations don’t have to rely on mutations within their own population;
The "but" sentence provides nothign to refute the prior sentence.
they can take advantage of all mutations, regardless of source. I didn’t think that this was something that ID would want to bring forward.
ID is not person that wants. But ID propoentns would want to discuss the exchange of pre-made genetic material that is not random, but already useful material. Darwinists still need to explain any pre-made useful genetic material. So, no, it is not good for Darwinists.JGuy_{August 1, 2014
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JGuy:
Are you suggesting transferred sequences have a historical origin that is not random
No.
Does this mean their origins are predestined natural sequences or even intelligently designed sequences?
No.
Anywaya, if you suggest these transferred sequences are evovled from Darwinian processes, then you have done nothing to make a case of non random mutation
I wasn't trying to make a case for non-random mutationsAcartia_bogart_{July 30, 2014
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hit should read hidJGuy_{July 30, 2014
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Acartia_bogart @ 5 Are you suggesting transferred sequences have a historical origin that is not random... Does this mean their origins are predestined natural sequences or even intelligently designed sequences? And how is this much different than co-opted sequences that have been discussed to length in this and other debating forums on ID vs. macroevolution. Anywaya, if you suggest these transferred sequences are evovled from Darwinian processes, then you have done nothing to make a case of non random mutation... you've simply hit the random mutation under a nutshell in the evolution game. Read ReMine's book.JGuy_{July 30, 2014
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This just makes Darwin's theory more valid (not that it needed it). The ID argument has always been that random mutations couldn't account for the variation that we see (again, not true). But now we see that populations don't have to rely on mutations within their own population; they can take advantage of all mutations, regardless of source. I didn't think that this was something that ID would want to bring forward.Acartia_bogart_{July 29, 2014
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OT: Illuminating the dark side of the genome - July 29, 2014 "Almost 50 percent of our genome is made up of highly repetitive DNA, which makes it very difficult to be analysed. In fact, repeats are discarded in most genome-wide studies and thus, insights into this part of the genome remained limited. Scientists from the Max Planck Institute of Immunobiology and Epigenetics (MPI-IE) in Freiburg now succeeded in examining this dark side of the genome. Their analyses revealed that repeat-associated heterochromatin is essential to repress retrotransposons and thereby protects the genomic integrity of stem cells. This work opens the way for future genome-wide analyses of repetitive regions in the genome and is in line with newly emerging functions for heterochromatin." http://phys.org/news/2014-07-illuminating-dark-side-genome.html Also of note, reanalyzing microRNAs confirms Kevin Peterson's conclusion from two years ago that microRNAs do not comport to the Darwinian tree of life. Flaws emerge in RNA method to build tree of life - Amy Maxmen - 28 July 2014 Study finds problems with alluringly simple way to tease out evolutionary relationships through microRNA. - Excerpt: Tiny molecules that seemed to provide a powerful way to construct the tree of life may not have such a strong capability after all. A team of scientists has exposed1 flaws in a previously celebrated method that uses molecules called microRNAs to deduce evolutionary relationships between animals.,,, MicroRNAs,, regulate the expression of genes, an essential duty that means that the genes that code for microRNAs are expected to remain mostly unchanged from generation to generation. This presumed conservation made microRNAs seem like ideal signatures for evolutionary relationships.,,, His team re-analysed four other microRNA studies on the trees that included flatworms3, vertebrates4, earthworms5 and some unusual parasites6. Similarly, the researchers noted many more microRNA losses than expected. "The way microRNAs were being analysed probably didn't reflect the way they evolve," says Thomson, whose team reports the latest analysis today in Proceedings of the National Academy of Sciences1.,,, ,,,Erik Sperling,., who was Peterson's co-author on some of the microRNA analyses2, 5, agrees with Thomson's conclusion that microRNAs cannot alone unveil species relationships. "MicroRNAs are not the panacea we perhaps originally hoped,” he says.,,, http://www.nature.com/news/flaws-emerge-in-rna-method-to-build-tree-of-life-1.15625 Talk about downplaying the problem, the problem from microRNAs is much more severe than they are letting on in that article. Here is Peterson from two years ago commenting on the microRNA problem for Darwinism,,, 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 pdf: http://www.nature.com/polopoly_fs/1.10885!/menu/main/topColumns/topLeftColumn/pdf/486460a.pdfbornagain77_{July 29, 2014
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I'd like to read ReMine's latest thoughts on this topic. Can you guys see if he would do a post?JGuy_{July 29, 2014
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Very interesting. Two possibilities occur to me: (a) Bacteria really do hoover up DNA passively and incorporate it willy-nilly, in which case most will die and few will be better-adapted. Or (b) They have some facility to pick and choose what they want, and where they will put it in their genome to be either active or silenced against some future need. Most will then survive to be studied. The latter is highly teleological, and suggests there is some "normality" (aka substantial form in the Aristotelian speak of Gerge Ellis or Vincent Torley)against which the bacteria make decisions. If cells collect blueprints, rather than blueprints defining cells, we're looking well outside the Neodarwinian box.Jon Garvey_{July 28, 2014
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Although I don't know how this new finding of 'environmental genes' fits in exactly, a year or so ago, Dr. Paul Nelson gave a talk on the overall organization of the bacterial genome:
,,,"Typical bacterial species. The smallest part of the pie are the genes that all bacteria share. 8% roughly. This second and largest slice (of the pie, 64%) are the genes that are specialized to some particular environment. They call them character genes. By far the biggest number of genes are the ones that are unique. This big green ball here (on the right of the illustration). These are genes found only in one species or its near relatives. Those are the ORFans (i.e. Genes with no ancestry). They said, on the basis of our analysis the genetic diversity of bacteria is of infinite size." Paul Nelson - quoted from 8:53 minute mark of the following video Widespread ORFan Genes Challenge Common Descent – Paul Nelson – video with references http://www.vimeo.com/17135166
You can see the pie chart that Dr. Nelson used in his talk here on page 108 of this following article:
Estimating the size of the bacterial pan-genome Excerpt Figure 2 pg. 108: At the genomic level, a typical bacterial genome is composed of 8% of core genes, 64% of character genes and 28% of accessory genes,,, http://www.paulyu.org/wp-content/uploads/2010/02/Estimating-the-size-of-the-bacterial-pan-genome.pdf
Also of interest, these new 'Orphan' genes in bacteria (and in fruit flies) are found to be just as essential as supposedly 'old' genes:
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. - per science mag
Finding ORFan genes, especially finding them early in embryonic development of fruit flies (and I would suppose other multicellular organisms), is extremely problematic for Darwinists since Embryo development (ontogeny) depends on developmental gene regulatory networks (dGRNs) and changes to DGRNs are 'always catastrophically bad'.
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 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/
Moreover, as if finding a large percentage of ORFan genes early in embryonic development was not bad enough for Darwinists, it is now found that the genetic code is not universal. Richard Dawkins about had a cow when he first learned from Craig Venter that the genetic code was not universal.
Dr. Craig Venter Denies Common Descent in front of Richard Dawkins! - video Quote: "I think the tree of life is an artifact of some early scientific studies that aren't really holding up.,, So there is not a tree of life. In fact from our deep sequencing of organisms in the ocean, out of, now we have about 60 million different unique gene sets, we found 12 that look like a very, very deep branching—perhaps fourth domain of life. " - Dr. Craig Venter, American Biologist involved in sequencing the human genome http://www.youtube.com/watch?v=MXrYhINutuI
In the following article, Dawkins gives the reason why a change to the genetic code would devastating to his preferred gradual evolution scenario,,,
Venter vs. Dawkins on the Tree of Life - and Another Dawkins Whopper - March 2011 Excerpt:,,, But first, let's look at the reason Dawkins gives for why the code must be universal: "The reason is interesting. Any mutation in the genetic code itself (as opposed to mutations in the genes that it encodes) would have an instantly catastrophic effect, not just in one place but throughout the whole organism. If any word in the 64-word dictionary changed its meaning, so that it came to specify a different amino acid, just about every protein in the body would instantaneously change, probably in many places along its length. Unlike an ordinary mutation...this would spell disaster." (2009, p. 409-10) http://www.evolutionnews.org/2011/03/venter_vs_dawkins_on_the_tree_044681.html
OK. Keep Dawkins' claim of universality in mind, along with his argument for why the code must be universal, and now look at what was found two months ago,,,
A glimpse into nature's looking glass -- to find the genetic code is reassigned: Stop codon varies widely - May 22, 2014 Excerpt: While a few examples of organisms deviating from this canonical code had been serendipitously discovered before, these were widely thought of as very rare evolutionary oddities, absent from most places on Earth and representing a tiny fraction of species. Now, this paradigm has been challenged by the discovery of large numbers of exceptions from the canonical genetic code,,, Approximately 99% of all microbial species on Earth fall in this category, defying culture in the laboratory but profoundly influencing the most significant environmental processes from plant growth and health, to the carbon and other nutrient cycles on land and sea, and even climate processes.,,, "We were surprised to find that an unprecedented number of bacteria in the wild possess these codon reassignments, from "stop" to amino-acid encoding "sense," up to 10 percent of the time in some environments," said Rubin. Another observation the researchers made was that beyond bacteria, these reassignments were also happening in phage, viruses that attack bacterial cells.,,, The punch line, Rubin said, is that the dogma is wrong. "Phage apparently don't really 'care' about the codon usage of the host. http://www.sciencedaily.com/releases/2014/05/140522141422.htm
It seems readily apparent to me that the more that is discovered about biological life the more extremely unlikely the materialistic myth of Darwinian evolution becomes. Verse and Music:
John 1:3 All things were made through him; and without him was not anything made that hath been made. Home Free - Ring of Fire (featuring Avi Kaplan of Pentatonix) [Johnny Cash Cover] https://www.youtube.com/watch?v=0l3dsHCScxU
bornagain77_{July 28, 2014
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