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How horizontal gene transfer has shaped the web of life


“using examples of HGT among prokaryotes, between prokaryotes and eukaryotes, and even between multicellular eukaryotes”

From Nature Reviews Genetics:, should feature many useful examples:

Here’s the abstract:

Horizontal gene transfer (HGT) is the sharing of genetic material between organisms that are not in a parent–offspring relationship. HGT is a widely recognized mechanism for adaptation in bacteria and archaea. Microbial antibiotic resistance and pathogenicity are often associated with HGT, but the scope of HGT extends far beyond disease-causing organisms. In this Review, we describe how HGT has shaped the web of life using examples of HGT among prokaryotes, between prokaryotes and eukaryotes, and even between multicellular eukaryotes. We discuss replacement and additive HGT, the proposed mechanisms of HGT, selective forces that influence HGT, and the evolutionary impact of HGT on ancestral populations and existing populations such as the human microbiome. (paywall) – Shannon M. Soucy, Jinling Huang and Johann Peter Gogarten

See also: Horizontal gene transfer: Sorry, Darwin, it’s not your evolution any more

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Hat tip: Pos-Darwinista

Question, can HGT be emperically proven or is it only inferred?. What is the best evidence for HGT? Mark M
Of related interest:
Endosymbiosis: A Theory in Crisis by Jeffrey P. Tomkins, Ph.D. * - Oct. 30, 2015 Excerpt: However, now that genome sequencing is inexpensive and widespread, the evolutionary story of endosymbiosis has become increasingly clouded and controversial. As new bacterial and eukaryotic genomes are sequenced and the proteins they encode are deduced, the whole evolutionary idea of endosymbiosis has been thrown into utter confusion. One of the most unexpected discoveries has been the utter lack of identified genes that would support the evolutionary tale. As stated in a recent paper, "What was not anticipated was how relatively few mitochondrial proteins with bacterial homologs [sequence similarity] would group specifically with ?-Proteobacteria in phylogenetic [evolutionary tree] reconstructions: At most, only 10–20% of any of the mitochondrial proteomes examined so far display a robust ?-proteobacterial signal.4" This lack of evidence for mitochondrial genes derived from bacterial origin in both the mitochondrial DNA and the genome contained in the cell’s nucleus, where most mitochondrial genes are located, is a serious problem for the evolutionary story.,,, http://www.icr.org/article/endosymbiosis-theory-crisis Tan, C. and J. Tomkins. 2015. Information Processing Differences Between Archaea and Eukarya—Implications for Homologs and the Myth of Eukaryogenesis. https://answersingenesis.org/biology/microbiology/information-processing-differences-between-archaea-and-eukarya/ Tan, C. and J. Tomkins. 2015. Information Processing Differences Between Bacteria and Eukarya—Implications for the Myth of Eukaryogenesis. https://answersingenesis.org/biology/microbiology/information-processing-differences-between-bacteria-and-eukarya/
A New Model for Evolution: A Rhizome - Didier Raoult - May 2010 Excerpt: Thus we cannot currently identify a single common ancestor for the gene repertoire of any organism.,,, Overall, it is now thought that there are no two genes that have a similar history along the phylogenic tree.,,,Therefore the representation of the evolutionary pathway as a tree leading to a single common ancestor on the basis of the analysis of one or more genes provides an incorrect representation of the stability and hierarchy of evolution. Finally, genome analyses have revealed that a very high proportion of genes are likely to be newly created,,, and that some genes are only found in one organism (named ORFans). These genes do not belong to any phylogenic tree and represent new genetic creations. http://darwins-god.blogspot.com/2010/05/new-model-for-evolution-rhizome.html
Didier Raoult, who authored the preceding paper, has been referred to as 'Most Productive and Influential Microbiologist in France'. He has said that Darwin’s theory is wrong.
The "Most Productive and Influential Microbiologist in France" Is a Furious Darwin Doubter - March 2012 Excerpt: Controversial and outspoken, Raoult last year published a popular science book that flat-out declares that Darwin's theory of evolution is wrong. http://www.evolutionnews.org/2012/03/the_most_produc057081.html Ribosome Excerpt: Ribosomes from bacteria, archaea and eukaryotes (the three domains of life on Earth) differ in their size, sequence, structure, and the ratio of protein to RNA. http://en.wikipedia.org/wiki/Ribosome LIFE: WHAT A CONCEPT! Excerpt: The ribosome,,,, it's the most complicated thing that is present in all organisms.,,, you find that almost the only thing that's in common across all organisms is the ribosome.,,, So the question is, how did that thing come to be? And if I were to be an intelligent design defender, that's what I would focus on; how did the ribosome come to be? George Church http://www.edge.org/documents/life/church_index.html Honors to Researchers Who Probed Atomic Structure of Ribosomes - Robert F. Service Excerpt: "The ribosome’s dance, however, is more like a grand ballet, with dozens of ribosomal proteins and subunits pirouetting with every step while other key biomolecules leap in, carrying other dancers needed to complete the act.” http://creationsafaris.com/crev200910.htm#20091010a Endoplasmic Reticulum: Scientists Image 'Parking Garage' Helix Structure in Protein-Making Factory - July 2013 Excerpt: The endoplasmic reticulum (ER) is the protein-making factory within cells consisting of tightly stacked sheets of membrane studded with the molecules (ribosome machines) that make proteins. In a study published July 18th by Cell Press in the journal Cell, researchers have refined a new microscopy imaging method to visualize exactly how the ER sheets are stacked, revealing that the 3D structure of the sheets resembles a parking garage with helical ramps connecting the different levels. This structure allows for the dense packing of ER sheets, maximizing the amount of space available for protein synthesis within the small confines of a cell. "The geometry of the ER is so complex that its details have never been fully described, even now, 60 years after its discovery," says study author Mark Terasaki of the University of Connecticut Health Center. "Our findings are likely to lead to new insights into the functioning of this important organelle.",,, ,, this "parking garage" structure optimizes the dense packing of ER sheets and thus maximizes the number of protein-synthesizing molecules called ribosomes within the restricted space of a cell. When a cell needs to secrete more proteins, it can reduce the distances between sheets to pack even more membrane into the same space. Think of it as a parking garage that can add more levels as it gets full.,,, http://www.sciencedaily.com/releases/2013/07/130718130617.htm
As well, The Ribosome of the cell is found to be very similar to a CPU in an electronic computer:
Dichotomy in the definition of prescriptive information suggests both prescribed data and prescribed algorithms: biosemiotics applications in genomic systems - 2012 David J D’Onofrio1*, David L Abel2* and Donald E Johnson3 Excerpt: The DNA polynucleotide molecule consists of a linear sequence of nucleotides, each representing a biological placeholder of adenine (A), cytosine (C), thymine (T) and guanine (G). This quaternary system is analogous to the base two binary scheme native to computational systems. As such, the polynucleotide sequence represents the lowest level of coded information expressed as a form of machine code. Since machine code (and/or micro code) is the lowest form of compiled computer programs, it represents the most primitive level of programming language.,,, An operational analysis of the ribosome has revealed that this molecular machine with all of its parts follows an order of operations to produce a protein product. This order of operations has been detailed in a step-by-step process that has been observed to be self-executable. The ribosome operation has been proposed to be algorithmic (Ralgorithm) because it has been shown to contain a step-by-step process flow allowing for decision control, iterative branching and halting capability. The R-algorithm contains logical structures of linear sequencing, branch and conditional control. All of these features at a minimum meet the definition of an algorithm and when combined with the data from the mRNA, satisfy the rule that Algorithm = data + control. Remembering that mere constraints cannot serve as bona fide formal controls, we therefore conclude that the ribosome is a physical instantiation of an algorithm.,,, The correlation between linguistic properties examined and implemented using Automata theory give us a formalistic tool to study the language and grammar of biological systems in a similar manner to how we study computational cybernetic systems. These examples define a dichotomy in the definition of Prescriptive Information. We therefore suggest that the term Prescriptive Information (PI) be subdivided into two categories: 1) Prescriptive data and 2) Prescribed (executing) algorithm. It is interesting to note that the CPU of an electronic computer is an instance of a prescriptive algorithm instantiated into an electronic circuit, whereas the software under execution is read and processed by the CPU to prescribe the program’s desired output. Both hardware and software are prescriptive. http://www.tbiomed.com/content/pdf/1742-4682-9-8.pdf
Raoult says not even ribosomal genes can be used as a golden standard for phylogeny:
Comparative genome analysis shows not only a substantial level of plasticity in the gene repertoire, but also provides evidence that nearly all genes, including ribosomal genes, have been exchanged or recombined at some point in time.
Mapou at 4, in at least one case, we know the mechanism: A bacterium uses a small "spear" to rummage for useful genes in a crustacean's shell. At least, that is what some of us would mean by a "mechanism." Seeing it at work amounts to an observation. News
HGT is a widely recognized mechanism for adaptation in bacteria and archaea.
Problem is, HGT is not a mechanism. It is an observation. One does not explain an observation by giving it a label and calling it a mechanism. This is not even wrong. It's not science. It's propaganda. PS. HGT was not predicted by Darwinism. Mapou
They showed that transfers are more frequent between closely related organisms.
We could use that to test the hypothesis that Zachriel is a spineless worm. :razz: Virgil Cain
Horizontal gene transfers were determined by their conflict with a reference phylogeny based on ribosomes. In other words, they are observed as anomalous against the background tree-pattern. They also showed that transfers are more frequent between closely related organisms. Zachriel
The following article goes through a bit of the history of how neo-Darwinists have come to use horizontal gene transfer to explain (away) contradictory patterns in the genetic evidence;
Evolutionists Celebrated This Prediction But When it Later Failed They Didn’t Care - Cornelius Hunter - April 2012 Excerpt: Sometimes their use of this lateral or horizontal gene transfer mechanism is a real stretch. And in any case, their story calls for evolution to have created this incredible mechanism which then was so important for adaptation and the supposed subsequent evolution. In other words, evolution created evolution.,,, In some cases evolutionists have no idea, beyond pure speculation, about how it could have happened. As they admit in one paper: "An alternative and more plausible possibility is that the STC gene has been laterally transferred among phylogenetically diverged eukaryotes through an unknown mechanism." http://darwins-god.blogspot.com/2012/04/evolutionists-celebrated-this.html Horizontal Gene Transfer 5-16-2015 by Paul Giem - video https://www.youtube.com/watch?v=W6X5sJ62NbE
Here is a recent article (2015) by Jeffrey Tomkins which shows that the mechanism of Horizontal Gene Transfer does not even begin to explain the dissimilarity in genomes being found:
Another Horizontal Gene Transfer Fairy Tale by Jeffrey P. Tomkins, Ph.D. - April 6, 2015 Excerpt: First, the researchers found unique genes in a variety of fruit flies, worms, primates, and humans that had no clear evolutionary ancestry. In other words, each of these genes is specific to a certain type of creature. Scientists have previously termed these "orphan genes"—a unique type of gene that provides a clear anti-evolutionary enigma I have discussed in previous reports.3,4 Some claim these novel orphan sequences evolved suddenly out of non-coding DNA while others, such as the authors of this new report, claim they were derived from HGT. The major problem with claiming that these alleged HGT genes are imported or "foreign" (i.e., transferred into the genome from some other creature), is that many of them encode important enzymatic proteins and are key parts of the interconnected gene networks and complex biochemical pathways that are essential to the very life of the organism. The researchers stated, "The majority of these genes are concerned with metabolism." Clearly, the genes are not foreign at all, but designed to function as key parts of essential biologically complex systems. Second, the approach to supposedly identifying many of the foreign genes in animals as microbial in origin was not even based on actual complete gene sequence, but depended upon isolated regions of similarity in the proteins they encode. In mammals, genes are quite complex, and on average only about 10% of the entire gene sequence actually codes for protein, the rest contains a large diversity of regulatory sequences that determine how the gene is to function and its various types of products. In contrast, microbial genes are typically much less complex and lack these intricate and intervening regulatory regions found in animal genes. If the researchers had actually compared the genomic DNA, very little similarity would have been discovered—in other words, they didn't do their homework correctly. In fact, they admitted their claim that the gene was foreign—or where it originated from—was purely hypothetical, when they stated that "absolute certainty in the assignment of most HGT is unachievable." Third, no mechanism of HGT for any of the hundreds of alleged "foreign genes" they found was either discovered or even suggested. This is due to the fact that the only cases where such gene transfer occurs in nature typically involves a clear host-parasite relationship. Not only that, but the cells of the germline (those that produce sperm and egg) must be specifically targeted or the introgressed genes (those that were incorporated from one species into the genome of another) will not be inherited. Unfortunately, evolutionary biologists constantly resort to fictional stories cloaked in technical terminology to escape the straightforward conclusion that the genomes of different creatures were purposefully crafted. Because of their unwavering commitment to evolution, all ideas about these cleverly designed and network-integrated gene sequences being engineered by a Creator are not considered—at least not openly. http://www.icr.org/article/another-horizontal-gene-transfer-fairy An Enzyme’s Phylogeny Reveals a Striking Case of Convergent Evolution – Jonathan M. – February 11, 2013 Excerpt: The authors attempt to account for the incongruity by positing that “the STC gene has been laterally transferred among phylogenetically diverged eukaryotes through an unknown mechanism.” They thus attribute the shared genes to horizontal gene transfer (with no offered mechanism), a proposition that has become a catch-all to explain away severe conflicts between evolutionary phylogenies.,,, “phylogenetic conflict is common, and frequently the norm rather than the exception” (Dávalos et al., 2012). Is it possible that the real reason for such striking and widespread phylogenetic discordance is that evolutionary biologists are looking at biology through the wrong lens? Could the reason that there is so much difficulty in correlating organisms to a tree be that no such tree exists? http://www.evolutionnews.org/2013/02/an_enzymes_phyl068911.html Horizontal gene transfer into humans? I am not convinced. - Jonathan Eisen, Professor at UC Davis. - March 12, 2015 http://phylogenomics.blogspot.com.br/2015/03/horizontal-gene-transfer-into-humans-i.html
This following paper shows that, even among single celled organisms, HGT transfer, rather than offering better resolution of the data, actually skews any hope evolutionists had of constructing a 'evolutionary tree' at even this base level of life, (and actually points to a method of 'designed' communication with single celled organisms 'talking' to each other:)
Biased gene transfer mimics patterns created through shared ancestry - 2010 http://www.pnas.org/content/107/23/10679.abstract
HGT is also found to be ‘non-random’
Don’t Judge Too Quickly - Fazale Rana - September 2010 Excerpt: Researchers long thought that the insertion of transposable elements into the genome took place at random locations, but recent work, including the efforts of the UT Arlington scientists, indicate that transposon insertion events are repeatable. (Thus suggesting an underlying 'designed mechanism' for explaining why some sequences are inserted at specific locations). Many people regard shared DNA sequences as the best evidence for evolution and common descent. But, as this recent work from UT Arlington demonstrates (along with other studies), there are other mechanisms beside common ancestry that can introduce the same DNA sequences in organisms unrelated via common descent. These types of studies indicate that evolution’s best evidence may not support it at all. (Similar sequences may very well be a consequence of some other type of mechanism, like parasite-mediated Horizontal Gene Transfer, as well as the result of common design). http://www.reasons.org/dont-judge-too-quickly

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