Humans are GMO ?!?!
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Patrik D'haeseleer
Mar 15, 2015, 8:15:14 PM3/15/15
to Shashank Goel, biocurious
Yeah, great study on horizontal gene transfer!
This is by no means the final word on the issue though - they still haven't done a good job at excluding possible contamination effects in genomes that are less well studied than human, or the alternative hypothesis that the seemingly anomalous phylogenetic inheritance patterns for these genes may be due to widespread gene loss:
"However, while the rate of gene loss over time can be estimated, at this point we cannot accurately estimate the rate of HGT over anything less than the time since the common ancestor of all metazoans, due to limited data."
Still, this study definitely points in the direction that HGT is not only far more common than we thought, but that many of these genes are indeed active and not just more "junk DNA".
Patrik
On Sun, Mar 15, 2015 at 3:24 PM, Shashank Goel <goel.cha...@gmail.com> wrote:
interesting research...GMP genetically modified people.--
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Geoff Ivison
Mar 15, 2015, 8:39:48 PM3/15/15
to Patrik D'haeseleer, Shashank Goel, biocurious
Thanks for some expert opinion Patrik! The headline seemed pretty wowwy...
Shashank Goel
Mar 16, 2015, 12:40:03 AM3/16/15
to Patrik D'haeseleer, biocurious
Thanks Patrik, True not home yet, more work needed for that thesis..but interesting nonetheless
can I assume all the sequencing activity of human microbiome may also add some data towards this notion..
-s
On Sun, Mar 15, 2015 at 5:15 PM, Patrik D'haeseleer <pat...@gmail.com> wrote:
Patrik D'haeseleer
Mar 19, 2015, 6:39:24 PM3/19/15
to Shashank Goel, biocurious
By the way, here are some comments by Jonathan Eisen detailing why he is not convinced about the horizontal gene transfer in humans story:
http://phylogenomics.blogspot.ca/2015/03/horizontal-gene-transfer-into-humans-i.html
Patrikhttp://phylogenomics.blogspot.ca/2015/03/horizontal-gene-transfer-into-humans-i.html
On Sun, Mar 15, 2015 at 5:15 PM, Patrik D'haeseleer <pat...@gmail.com> wrote:
Tristan Eversole
Apr 4, 2015, 4:14:35 PM4/4/15
to Patrik D'haeseleer, biocu...@googlegroups.com
I haven’t read the paper yet, to be honest, but I feel like Eisen was going easy on them.
The ever-caustic Dan Graur, however, does not disappoint: http://judgestarling.tumblr.com/post/114111584916/big-news-rampant-horizontal-gene-transfer-into
I think that the trouble here is that phylogenetic inference methods assume that the characters you give them are the product of descent with modification, i.e. that they’re homologous. Detecting other processes, such as horizontal transfer, is a matter of showing that the characters in the analysis do not fit this assumption(*). (In what sense do phylogenetic trees provide evidence for evolution? Well, changes in character states between taxa generally fit the hypothesis of common descent unreasonably well— that would be my answer.) This means that you have to be very careful to differentiate between “we’ve found strong evidence of horizontal transfer” and “we’ve done a terrible phylogenetic study.” Using software to build trees is easy. Doing a good phylogenetic analysis is not.
For some reason, people seem to really want horizontal transfer between multicellular eukaryotes to exist. The transposon Space Invader provides a well-supported case where this may have happened, but I have yet to encounter any good evidence suggesting that horizontal transfer between eukaryotes is a common event. Additionally, I am generally skeptical of claims along the following lines:
1) Some highly novel genomic process has been found in humans which
2) is claimed to have adaptive value but
3) doesn’t involve the nervous system, body hair, or something else which we might reasonably expect to be different between humans and other taxa, or for which the authors provide only a speculative connection to such, and
4) is supported largely or entirely by indirect evidence.
I don’t mean that such discoveries don’t happen; after all, alternative splicing was discovered in viruses, miRNA was discovered in nematodes, etc… I’m just wary of that cluster of assertions.
—Tristan
*Here I have to admit that I don’t know what the phylogenetic network theory people are doing, so I can’t tell you how they approach this issue.
The ever-caustic Dan Graur, however, does not disappoint: http://judgestarling.tumblr.com/post/114111584916/big-news-rampant-horizontal-gene-transfer-into
I think that the trouble here is that phylogenetic inference methods assume that the characters you give them are the product of descent with modification, i.e. that they’re homologous. Detecting other processes, such as horizontal transfer, is a matter of showing that the characters in the analysis do not fit this assumption(*). (In what sense do phylogenetic trees provide evidence for evolution? Well, changes in character states between taxa generally fit the hypothesis of common descent unreasonably well— that would be my answer.) This means that you have to be very careful to differentiate between “we’ve found strong evidence of horizontal transfer” and “we’ve done a terrible phylogenetic study.” Using software to build trees is easy. Doing a good phylogenetic analysis is not.
For some reason, people seem to really want horizontal transfer between multicellular eukaryotes to exist. The transposon Space Invader provides a well-supported case where this may have happened, but I have yet to encounter any good evidence suggesting that horizontal transfer between eukaryotes is a common event. Additionally, I am generally skeptical of claims along the following lines:
1) Some highly novel genomic process has been found in humans which
2) is claimed to have adaptive value but
3) doesn’t involve the nervous system, body hair, or something else which we might reasonably expect to be different between humans and other taxa, or for which the authors provide only a speculative connection to such, and
4) is supported largely or entirely by indirect evidence.
I don’t mean that such discoveries don’t happen; after all, alternative splicing was discovered in viruses, miRNA was discovered in nematodes, etc… I’m just wary of that cluster of assertions.
—Tristan
*Here I have to admit that I don’t know what the phylogenetic network theory people are doing, so I can’t tell you how they approach this issue.
Tristan Eversole
Apr 10, 2015, 7:58:07 PM4/10/15
to Patrik D'haeseleer, biocu...@googlegroups.com
I’d just like to add one more comment on this article.
Eisen notes that they haven’t provided their alignments:
> I find it impossible to judge the quality of this paper without being able to see the alignments they used for each phylogenetic tree. I cannot find alignments for the trees even after going to their Figshare site with the trees. I therefore think there is not much to say about the paper until being able to see those.
This is a lamentably common practice in the systematics community. Lots of authors don’t provide their trees or alignments, and the main existing archive for trees and alignments, TreeBASE, is terrible. Drew et al. (2013) provide a damning indictment of the state of the field:
> Surprisingly, only 16.7%, 1,262 from a total of 7,539 publications surveyed, provided accessible alignments/trees (Figures 1 and 2). Our attempts to obtain datasets directly from authors were only 16% successful (61/375; see Table S4), and we estimate that approximately 70% of existing alignments/trees are no longer accessible. Thus, we conclude that most of the underlying sequence alignments and phylogenetic trees produced by the systematic community during the past several decades are essentially lost, accessible only as static figures in a published journal article with no capacity for subsequent manipulation. Furthermore, when data are deposited, they are often incomplete (e.g., what characters were excluded, accepted taxon names; see Text S1 and Figure S1). Our survey of publications that implemented BEAST revealed that only 11 out of 100 (11%) examined studies provided access to the underlying xml input file, which is critical for reproducing BEAST results. Although funding agencies often require all data to be accessible from funded publications, our results reveal this is more the exception than the rule.
Drew, B. T., Gazis, R., Cabezas, P., Swithers, K. S., Deng, J., Rodriguez, R., et al. (2013). Lost branches on the tree of life. PLoS Biology, 11(9), e1001636. doi:10.1371/journal.
—Tristan
Eisen notes that they haven’t provided their alignments:
> I find it impossible to judge the quality of this paper without being able to see the alignments they used for each phylogenetic tree. I cannot find alignments for the trees even after going to their Figshare site with the trees. I therefore think there is not much to say about the paper until being able to see those.
This is a lamentably common practice in the systematics community. Lots of authors don’t provide their trees or alignments, and the main existing archive for trees and alignments, TreeBASE, is terrible. Drew et al. (2013) provide a damning indictment of the state of the field:
> Surprisingly, only 16.7%, 1,262 from a total of 7,539 publications surveyed, provided accessible alignments/trees (Figures 1 and 2). Our attempts to obtain datasets directly from authors were only 16% successful (61/375; see Table S4), and we estimate that approximately 70% of existing alignments/trees are no longer accessible. Thus, we conclude that most of the underlying sequence alignments and phylogenetic trees produced by the systematic community during the past several decades are essentially lost, accessible only as static figures in a published journal article with no capacity for subsequent manipulation. Furthermore, when data are deposited, they are often incomplete (e.g., what characters were excluded, accepted taxon names; see Text S1 and Figure S1). Our survey of publications that implemented BEAST revealed that only 11 out of 100 (11%) examined studies provided access to the underlying xml input file, which is critical for reproducing BEAST results. Although funding agencies often require all data to be accessible from funded publications, our results reveal this is more the exception than the rule.
Drew, B. T., Gazis, R., Cabezas, P., Swithers, K. S., Deng, J., Rodriguez, R., et al. (2013). Lost branches on the tree of life. PLoS Biology, 11(9), e1001636. doi:10.1371/journal.
—Tristan
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