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The Edge of Horizontal Gene Transfer

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Horizontal Gene Transfer (HGT) is now being invoked fairly often as a magic wand by Darwinists. So what experimental evidence do we have?

Genome-Wide Experimental Determination of Barriers to Horizontal Gene Transfer

Horizontal gene transfer, in which genetic material is transferred from the genome of one organism to another, has been investigated in microbial species mainly through computational sequence analyses. To address the lack of experimental data, we studied the attempted movement of 246,045 genes from 79 prokaryotic genomes into Escherichia coli and identified genes that consistently fail to transfer. We studied the mechanisms underlying transfer inhibition by placing coding regions from different species under the control of inducible promoters. Our data suggest that toxicity to the host inhibited transfer regardless of the species of origin and that increased gene dosage and associated increased expression may be a predominant cause for transfer failure. While these experimental studies examined transfer solely into E. coli, a computational analysis of gene transfer rates across available bacterial and archaeal genomes supports that the barriers observed in our study are general across the tree of life.

To summarize, they tested a small subset of the genes that were classified as nontransferable (0.6%). Out of the genes they tested, 80% could not be artificially transferred when in an active state, most of which were related to the ribosome. So, this would suggest that less than 0.5% of genes were toxic. However, from what I’ve read elsewhere things are even more grim for HGT as a Darwinian mechanism for major innovation when it comes to higher species.

Bacterial type III secretion systems are ancient and evolved by
multiple horizontal-transfer events

Type III secretion systems (TTSS) are unique bacterial mechanisms that mediate elaborate interactions with their hosts. The fact that several of the TTSS proteins are closely related to flagellar export proteins has led to the suggestion that TTSS had evolved from flagella. Here we reconstruct the evolutionary history of four conserved type III secretion proteins and their phylogenetic relationships with flagellar paralogs. Our analysis indicates that the TTSS and the flagellar export mechanism share a common ancestor, but have evolved independently from one another. The suggestion that TTSS genes have evolved from genes encoding flagellar proteins is effectively refuted. A comparison of the species tree, as deduced from 16S rDNA sequences, to the protein phylogenetic trees has led to the identification of several major lateral transfer events involving clusters of TTSS genes. It is hypothesized that horizontal gene transfer has occurred much earlier and more frequently than previously inferred for TTSS genes and is, consequently, a major force shaping the evolution of species that harbor type III secretion systems.

Notice that HGT is also used as a workaround to claim that the type III secretion system appeared in nature before the flagellum. Which of course is in competition with the scenario preferred by ID proponents by which the flagellum came first and the TTSS derived from it. But even going with the scenario the Darwinists prefer the same complex mechanism has to evolve at least TWICE (as in, evolved once and transferred successfully in a functional state that gives survival advantage). Note that HGT is only a method for transferring previously derived information, not the source of the information itself. The hope is that combinational effects will do their magic.

We can look to the National Research Council to see why this is important:

“Natural selection based solely on mutation is probably not an adequate mechanism for evolving complexity.
More important, lateral gene transfer and endosymbiosis are probably the most obvious mechanisms for creating complex genomes…”

Now that we have actual experimental data we can apply them to previous speculations. Back when Behe’s Edge of Evolution came out I commented that the next step for ID researchers is to do experiments to discover the exact limitations of all proposed Darwinian mechanisms. I’d specifically like to see researchers artificially transfer the genes related to the flagellum to other species and see if they help, kill, harm, or inhibit the new hosts. As this data indicates, they are likely to be “capable” of being transferred in general but that still does not validate their story-telling. Also, while research related to ID icons like the flagellum are interesting I’d rather see further research into the limitations of HGT when it comes to higher species.

[...] 24th, 2007 · 1 Comment On Uncommon Descent, Patrick has a post on a paper that probes the barriers to horizontal gene transfer. In the comments, a commenter named Bob O’H makes the case that less than 0.5% of genes were [...] Horizontal Transfer in E. Coli « Professor Smith’s Weblog
bornagain, Sorry, I don't have a subscription...does anyone else here on UD? Patrick
Patrick; This is The only partial reference I could find, and I can't open the page: A deleterious effect is likely to be the outcome of the majority of HGT events occurring from transgenic plants as well, but rare beneficial events cannot ... http://www.nature.com/nbt/journal/v22/n9/full/nbt1006.html It would be nice to have a hard number for deleterious HGT rate if you can get it, but it is really beside the point since SNPs are proven to be overwhelming detrimental. bornagain77
The paper is about why certain genes fail to consistently transfer between other bacteria and E. Coli, but this number of genes is apparently less than .5% of the 246,000 studied. So they found that the vast majority of bacterial genes studied do apparently readily transfer into E. Coli. This actually might support the inflated claims about HGT in evolution, except that it doesn't deal with some other important factors that come to mind. The most important would seem to be that HGT doesn't trump Dembski's No Free Lunch with regard to complex specified information in the genome. Some organism has to develop the gene in the first place, before it can be transferred. The same goes for gene duplication in recombination, another favorite magic wand. For higher organisms structure and behavior is becoming to be understood in epigenetic terms involving complicated developmental programs. HGT doesn't seem likely to be much of a factor in this because much of the information isn't even in the formally defined genes. magnan
Patrick, I would still like to have a figure to put on the deleterious rate to horizontal gene transfers HGTs,,,My gut feeling is that it will approach 100% since up to 99.9999% is established for single nucleotide polymorphisms by Garrish, Lenski 1998, as well the biological big bang (BBB) recently put forth: http://www.biology-direct.com/content/2/1/21 Depends heavily on HGTs, so having a hard number could effectively crush the evolutionists day dreaming on this matter. bornagain77
This site is interesting in relation to the topic. http://www.creationontheweb.com/content/view/5067/ of special note: Comparisons of the DNA sequence data from the recently sequenced genomes, which have been determined by testable and repeatable scientific means, conflict with Darwin’s single evolutionary tree of life. As a result, polyphyly, in one sense the opposite of evolution or common ancestry, has been embraced in the form of (horizontal transfer)HT and a community of ancestral cells. This is not surprising, as ReMine predicted that evolutionary ideology is bound to naturalism and simply ‘accommodates’ all evidence to fit reworked evolutionary s, thus showing that it is not falsifiable and therefore not scientific according to science philosopher Carl Popper’s primary criterion.12 He even predicted that evolutionists would increasingly resort to such lateral transfer. bornagain77
Well the article suggests two things: 1) Genome-sequencing projects should no longer be discarding Bacterial DNA when assembling invertebrate genomes. 2)The wolbachia could be the next mitochondria....everyone will may have a wolbachia organelle. Whatever the case we can no longer assume contamination in regard to bacterial DNA. Tina
Here is the article Tina is talking about http://www.rochester.edu/news/show.php?id=2963 of special note: Clark confirmed that the wolbachia genes are inherited like "normal" insect genes in the chromosomes, and Dunning-Hotopp showed that some of the genes are "transcribed" in uninfected flies, meaning that copies of the gene sequence are made in cells that could be used to make wolbachia proteins. Function unknown at this time. My bet is both, bacteria and genome sequence will have function. In regards to the ID/'evolution debate: Is this characteristic found in the human genome? In the early days of the Human Genome Project, some studies appeared to show bacterial DNA residing in our own genome, but those were shown indeed to be caused by contamination. Wolbachia is not known to infect any vertebrates such as humans. bornagain77
A recent public release from the University Of Rochester discusses findings based on "one species' genome discovered inside another's" (absorbed - integrated - heritable). The interesting thing about this article is the emphasis it places on the discovery as raising "questions about evolution" and "posing dramatic implications for evolution". Lateral gene transfer can reinforce the Intelligent Design argument and may even eventually explain "camouflage" in the sense that the organism is able to "imbibe" DNA from the environment it inhabits to enable it to survive in that environment. Thats Intelligent Design to me. Tina
Thanks. Should have edited this more in the first place to be clearer... Patrick
Go ahead. Bob Bob O'H
That's a much better summarization, Bob. Mind if I use it in the main body of the page? Patrick
In short, over 80 percent of the genes tested stopped E. coli from growing, meaning that when transferred across species they are toxic to their new hosts.
If I'm reading the paper correctly, this is 80% of the genes they tested, which they selected because they had been marked as untransferable (top of second column, p2). However, only 1402 of 246045 genes (=0.6%) were classified as untransferable. So, this would suggest that less than 0.5% of genes were toxic. Bob Bob O'H
They might latch onto that 20% figure but it's the origination of the original information they have yet to explain in any case. Not to mention that 20% is not a general figure, like 4/5 just randomly fail to transfer successfully. I should have been more clear about that in my comment. They were analyzing sequence data from 79 species and they identified over 600 genes that don't transfer easily into E. coli. Most of the genes are intrinsically resistant to transferring, apparently. Many code for parts of the ribosome. The researchers modified the genes so they could turn them on or off. When in the off state they could be tolerated but that 80% figure refers to the rejection that occurred when they were active. So, no, that 20% does not refer to "increased complexity that increased its fitness to survive" as far as I'm aware. I think I'll remove that little comment to prevent confusion... Patrick
Patrick you mention, In short, over 80 percent of the genes tested stopped E. coli from growing, This is all fine and well, but seeing as evolutionists will use any sort of suggestive evidence they can get there hands on, Can you please elaborate on what the other 20% did,,,i.e. Did the other 20% of HGT genes studied give the E. coli any sort of increased complexity that increased its fitness to survive? bornagain77

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