5 ms·

Claim that tardigrades got 1/6 of DNA from microbes is starting to unravel

30 points by r0muald 11y ago

carbocation 11y ago
This leads off a series of tweets from the Edinburgh team evaluating the read data with some informative images: https://twitter.com/sujaik/status/671758970982416385 https://twitter.com/sujaik/status/671758970982416385
FeepingCreature 11y ago
Fuck this narrative of rivalry. Scientists working in the same field have put out a study that disagrees with the first study. This is not a severe blow, it does not debunk the first study, it does not imply some sort of rivalry. Science is cooperative. We all want to find the truth.
- tosseraccount 11y ago
  PNAS Paper (the firs paper) is here : http://www.pnas.org/content/early/2015/11/18/1510461112.abstract http://www.pnas.org/content/early/2015/11/18/1510461112.abst... : "Evidence for extensive horizontal gene transfer from the draft genome of a tardigrade". The gene transfer angle is the most prominent thrust of the paper: "Horizontal gene transfer (HGT), or the transfer of genes between species, has been recognized recently as more pervasive than previously suspected. Here, we report evidence for an unprecedented degree of HGT into an animal genome, based on a draft genome of a tardigrade, Hypsibius dujardini." Non target contamination in sequencing DNA and RNA is common. Attributing "horizontal gene transfer" due to the "noise" is a mistake. The second group actually does debunk the initial paper's main point. Perhaps establishment science need to move the peer review from before publication to after.
  - jkyle 11y ago
    > Perhaps establishment science need to move the peer review from before publication to after. The after publication 'peer review' is when colleagues attempt to replicate your findings. It's a series of gates to credibility and general acceptance, not a single door.
- stefantalpalaru 11y ago
  > Science is cooperative. We all want to find the truth. You'd think so, but no. Scientists want to get funded, and getting their work invalidated like this is a problem. So is making enemies among those that will review your articles in the near future. That's why contradictions are usually softened and hidden behind praises of unrelated parts of the work - they're all in it together and they need to cooperate in order to keep getting grants. You'll usually find honest criticism in informal conversations, not published for all to see.
stefantalpalaru 11y ago
Is there a way to get just the DNA you're interested in sequencing in the first place? Eliminating the sequences that look out of place afterwards does not seem like a good strategy.
- GFK_of_xmaspast 11y ago
  Supposing there was, why wouldn't they have done that?
  - stefantalpalaru 11y ago
    Cost.
- noname123 11y ago
  Sequencing is typically done in "whole-genome shotgun" fashion; or imagine, if you shred a 100pg document (lyse and extract DNA, Illumina sequencing) into 100 lettered fragments, and have gathered all of the fragments of 1000 copies of this shredded document, some of them are regular words in forward orientation and some of them have every letter reversed (reverse strand since DNA is complementary double-stranded); The fragments given the nature of the shredder are all shredded slightly at different places and they are all mixed up - so you have to piece together like a jigsaw puzzle into a single copy (genome assembly). However suppose there are lots of palindromic repeats in the document like the phrase "stressed" repeated 100 times such that they exceed your individual 100 lettered fragment, or is it the palindrome dopleganger "desserts" repeated 100 times? Or a mix of "stressed desserts" repeated in different ways 100 times? And also what of the phrases before and after "stressed/desserts," how do you place them since you are not sure about the order/orientation of this repeat? This is the challenge of genome assembly. Now having more copies of the shredded document helps but some repeats are very nasty and aligning them in the assembly is not statistically tractable. And also they don't necessarily encode for relevant genes so they are often filtered out. Furthermore, they are arguably the regions of the DNA that is the most prone to change, since you can think of them as the "filler text" of the document; if an important part of the document is unintelligible, then this document wouldn't survive nature's QC process of sexual selection. However, unintelligible parts of the document don't encode important genes, so they evolve very quickly because they have a higher tolerance of typo's and mutations. So in an population pool that people use to assemble and come up with an consensus genome (keep in mind the population pool will have different gene variation), so it may turn out at a particular base pair position in the document, there is so much variation that the genome assembler can't conclusively come up with an consensus sequence or a reasonable distribution of base pair (A, T, C, G).

30 points by r0muald 11y ago

This leads off a series of tweets from the Edinburgh team evaluating the read data with some informative images: https://twitter.com/sujaik/status/671758970982416385 https://twitter.com/sujaik/status/671758970982416385

FeepingCreature 11y ago

Fuck this narrative of rivalry. Scientists working in the same field have put out a study that disagrees with the first study. This is not a severe blow, it does not debunk the first study, it does not imply some sort of rivalry. Science is cooperative. We all want to find the truth.

tosseraccount 11y ago
PNAS Paper (the firs paper) is here : http://www.pnas.org/content/early/2015/11/18/1510461112.abstract http://www.pnas.org/content/early/2015/11/18/1510461112.abst... : "Evidence for extensive horizontal gene transfer from the draft genome of a tardigrade". The gene transfer angle is the most prominent thrust of the paper: "Horizontal gene transfer (HGT), or the transfer of genes between species, has been recognized recently as more pervasive than previously suspected. Here, we report evidence for an unprecedented degree of HGT into an animal genome, based on a draft genome of a tardigrade, Hypsibius dujardini." Non target contamination in sequencing DNA and RNA is common. Attributing "horizontal gene transfer" due to the "noise" is a mistake. The second group actually does debunk the initial paper's main point. Perhaps establishment science need to move the peer review from before publication to after.
- jkyle 11y ago
  > Perhaps establishment science need to move the peer review from before publication to after. The after publication 'peer review' is when colleagues attempt to replicate your findings. It's a series of gates to credibility and general acceptance, not a single door.
stefantalpalaru 11y ago
> Science is cooperative. We all want to find the truth. You'd think so, but no. Scientists want to get funded, and getting their work invalidated like this is a problem. So is making enemies among those that will review your articles in the near future. That's why contradictions are usually softened and hidden behind praises of unrelated parts of the work - they're all in it together and they need to cooperate in order to keep getting grants. You'll usually find honest criticism in informal conversations, not published for all to see.

stefantalpalaru 11y ago

Is there a way to get just the DNA you're interested in sequencing in the first place? Eliminating the sequences that look out of place afterwards does not seem like a good strategy.

GFK_of_xmaspast 11y ago
Supposing there was, why wouldn't they have done that?
- stefantalpalaru 11y ago
  Cost.
noname123 11y ago
Sequencing is typically done in "whole-genome shotgun" fashion; or imagine, if you shred a 100pg document (lyse and extract DNA, Illumina sequencing) into 100 lettered fragments, and have gathered all of the fragments of 1000 copies of this shredded document, some of them are regular words in forward orientation and some of them have every letter reversed (reverse strand since DNA is complementary double-stranded); The fragments given the nature of the shredder are all shredded slightly at different places and they are all mixed up - so you have to piece together like a jigsaw puzzle into a single copy (genome assembly). However suppose there are lots of palindromic repeats in the document like the phrase "stressed" repeated 100 times such that they exceed your individual 100 lettered fragment, or is it the palindrome dopleganger "desserts" repeated 100 times? Or a mix of "stressed desserts" repeated in different ways 100 times? And also what of the phrases before and after "stressed/desserts," how do you place them since you are not sure about the order/orientation of this repeat? This is the challenge of genome assembly. Now having more copies of the shredded document helps but some repeats are very nasty and aligning them in the assembly is not statistically tractable. And also they don't necessarily encode for relevant genes so they are often filtered out. Furthermore, they are arguably the regions of the DNA that is the most prone to change, since you can think of them as the "filler text" of the document; if an important part of the document is unintelligible, then this document wouldn't survive nature's QC process of sexual selection. However, unintelligible parts of the document don't encode important genes, so they evolve very quickly because they have a higher tolerance of typo's and mutations. So in an population pool that people use to assemble and come up with an consensus genome (keep in mind the population pool will have different gene variation), so it may turn out at a particular base pair position in the document, there is so much variation that the genome assembler can't conclusively come up with an consensus sequence or a reasonable distribution of base pair (A, T, C, G).