Does horizontal gene transfer enable genetic parasites to survive natural selection?

3 Replies to “Does horizontal gene transfer enable genetic parasites to survive natural selection?”

1. 1
   DATCG says:

   August 10, 2018 at 10:33 pm

   Hmmmmm, a guestion.

   How sure is the evidence for HGT as a blind, unguided factor of neo-darwinian evolution for humans?

   Here’s a paper in 2017 that finds flaws with such attributions of HGT assignments in humans by an original research challenging claims, assumptions and maybe bad research at NCBI(National Center for Biotechnology Information). It’s quite illuminating to see the call out by one researcher against another, as well as what appears to be shabby research?

   I recommend people read this…
   Horizontal gene transfer is not a hallmark of the human genome

   Steven L. Salzberg; Genome Biology May 8, 2017

   How much is assumptions based?

   Abstract

   Crisp et al. recently reported that 145 human genes have been horizontally transferred from distant species. Here, I re-analyze those genes listed by Crisp et al. as having the highest certainty of having been horizontally transferred, as well as 17 further genes from the 2001 human genome article, and find little or no evidence to support claims of horizontal gene transfer (HGT).

   more from Introduction…

   Their reanalysis, which was based on a combination of BLAST searches and phylogenetic trees, identified hundreds of “foreign” genes in animals; this led them to claim that HGT “has occurred on a previously unsuspected scale in metazoans” and that it is a significant factor in animal evolution.

   In this study, I re-examined the claims of Crisp et al. [1] focusing on the human genes. Instead of using a large-scale, automated analysis, which by its very nature could enrich the results for artifactual findings, I looked at each human gene individually to determine whether the evidence is sufficient to support the conclusion that HGT occurred.

   An important principal here is that extraordinary claims require extraordinary evidence: there is no doubt that the vast majority of human genes owe their presence in the human genome to the normal process of inheritance by vertical descent.

   Thus, if other, more mundane processes can explain the alignments of a human gene sequence, these explanations are far more likely than HGT.

   Interesting that blind, unguided evolution by vertical descent is considered “mundane” as an explanation.

   But what did he find?

   Results

   For my re-analysis, I re-aligned the 17 human genes that were originally reported as having undergone bacterial-vertebrate transfer (BVT), a finding that has been rejected by our work[3] and that of others [4, 5], but re-claimed by Crisp et al.[1](Table 1).

   I found that the evidence does not support HGT for any of them.

   What is going on in research science these days? Was it all assumptions by Crisp et al.?

   Salzberg continues…

   (One important point worth noting here is that Crisp et al. listed some of these genes as “confirmed” by Salzberg et al. [3].

   This was not the case; our previous study invalidated most of the previously claimed HGT events, but was not able to dismiss all of them.

   Our study made it clear that we did not consider the presence of the remaining genes to be the result of HGT events.)

   Crisp et al.[1] reported a total of 145 human genes that they claimed to be the result of HGT; 39 of these are labeled in their highest confidence group, class A.

   Of these 39, seven are included in the first group of 17, leaving 32 newly claimed HGT events.

   I examined these 32 class A genes (Table 2) and again find no evidence for HGT.

   What a knock down of HGT claims of one scientist(et al.) by another scientist. Good to see.

   Who is correct? Are HGT claims built upon assumptions? As in this case knocked down by original research scientist Steven L. Salzberg?

   GIGO – Garbage In Garbage Out?

   Results

   Of the 17 genes from the original human genome paper that Crisp et al. [1] claim are true examples of HGT, my analysis finds that 12 genes fail to pass the authors’ own BLAST-based test for HGT, because their closest metazoan match has a bitscore that is greater than the best non-metazoan match (Table 1).

   Of the 28 genes representing new claims of HGT (Table 2), 26 fail the initial screen for HGT candidates, either because they fail the original BLAST bitscore test, because they represent contaminants in draft genomes, or because they are known mitochondrial or retrotransposed genes.

   The remaining seven genes (five from Table 1 and two from Table 2) include three close paralogs (HAS1–3) and thus represent four hypothesized HGT events.

   A combination of gene loss and evolutionary rate variation is more than adequate to explain these genes: among other reasons, the alignments and bitscores are the result of screening more than 20,000 human genes, and one might expect a few genes from this large set to be lost (or to have evolved slightly more rapidly) in the non-chordate genomes.

   One reason that better BLAST results were found in the current study could well be that this study used data from May 2016, whereas Crisp et al.’s study used data from January 2013. (Edit GIGO)

   A large number of additional genomes have been deposited in public archives during the three years between the two analyses.

   These species were not available to the previous study and thus the orthologous genes from these taxa were missed.

   Insofar as this explanation is correct, it strengthens the argument for gene loss as the explanation for the (very few) human genes that still have better BLAST matches in non-metazoans than in non-chordate metazoans.

   Wow! So, assumptions prior to having all the data?

   This is interesting research work and rebuttals to what appears to be typical assumptions based answers.
2. 2
   DATCG says:

   August 10, 2018 at 10:38 pm

   Hopefully, GPuccio and others may comment and add their thoughts on HGT? In as far as an “unguided, blind” Darwinist type assumption?

   Some thoughts.

   It’s one thing to see patterns, quite another to attribute those patterns to past blind events without being able to actually test the claims.

   And yet quite another to still not realize we do not have all the Data, let alone accurate data we need to build upon for claims of HGT of large scale in humans?

   I don’t have all the answers, but curious what others think. Salzberg points out flaws based upon bad raw data input as a result of previous inferior collections and technology.

   Our ability to ascertain any truth at all in genomics is then questionable for either side of this debate to some extent if the raw data input for testing is not a complete picture.

   So if assumptions were indeed made and he is correct, then once again, the claims do not match up for Darwinist Theory(blind, unguided vs Design). And we see how bad data or not enough data can fail if raw input data is suspect or missing altogether.

   Salzberg then points back to the original vertical evolution claims which I do not seek to argue to much here at this point.

   Only that I think this type of response by him to other researchers on HGT Claims in humans should be noticed and robustly reviewed and discussed by Design Theorist on all sides of the debate.

   Does HGT save the Darwinist and therefore their blind appeals to it to save the day? What is left if HGT is not accurate as Salzberger states for humans in terms of ability for blind, unguided evolution to survive as a legitimate theoretic construct of reality based science research?
3. 3
   Nonlin.org says:

   August 11, 2018 at 7:21 am

   “Natural Selection” is one of the most retard concepts ever… and it’s a huge mystery how NS can fool so many otherwise intelligent people for so long: http://nonlin.org/natural-selection/
   The five ridiculous claims of “natural selection”
   1. “Design by multiple choice” is ridiculous
   2. “Multiple choice from ALL random answers” is ridiculous
   3. “Designing without trying” is ridiculous
   4. “Self design” is ridiculous
   5. “Design by incremental optimization” is ridiculous

   Summary:
   1. Natural Selection concept fails since phenotype does not determine survival which is also tautological with “best adapted”
   2. “Blind, mindless, purposeless, natural, and process” qualifiers fail
   3. Phenotype is an unstable infinite set (hence unknowable and theoretical)
   4. Fitness concept is redundant since never defined independently of survival
   5. “Selection” is Survival
   6. The only selection is Intelligent Selection – always done by an Intelligent Selector
   7. Selection is limited to a narrow set of adaptations – one cannot selected what is not there
   8. Selection and Mutations lack creativity, therefore cannot explain body designs
   9. We do not observe “divergence of character” but ‘limited variations around a mean’
   10. Extinct organism were not flawed and their features were not “selected away”
   11. Intelligent Selection should replace Natural Selection but only if we ever transmutate organisms
   12. Humans do not apply Natural Selection because it doesn’t work
   13. Designs must cross an inevitable optimization gap making evolution impossible
   14. Breeding is much more than “artificial selection” and unrelated to any natural process

   “Natural selection” proponents must answer these simple questions – pick any biologic entity including populations and give the 80/20 Pareto without too much accuracy or precision :
   1. What is that biologic entity’s phenotype?
   2. What is its environment?
   3. What is its fitness function?
   4. What is the relationship between its phenotype, environment, fitness, and survival/reproductive success?