Saturday, March 09, 2013

Ugg - story about gene transfer/evolution based on NSF press release has a NASA-esque smell

Well, this made me cringe many many times: Extreme Algae Thieves Its Genes From Bacteria - Science News - redOrbit: Science

The article discusses a new paper which itself sounds potentially interesting.  The paper itself sounds somewhat interesting.  But that is besides the point.  The parts that made me cringe are the inaccurate or overhyped statements about the novelty of this work.  Here are some of the statements I find troubling
  • "While the ability to pilfer genes from another microorganism has been seen before, scientists have never observed this ability in a eukaryote – an organism with a nucleus."  
    • Wow.  Completely ludicrous.  There are hundreds if not thousands of papers on lateral gene transfer to organisms with nuclei.  
  • “The results give us new insights into evolution,” said co-author Gerald Schoenknecht of Oklahoma State University’s Department of Botany. “Before this, there was not much indication that eukaryotes acquire genes from bacteria.”
    • Same complaint as above. 
  • "The age of comparative genome sequencing began only slightly more than a decade ago, and revealed a new mechanism of evolution – horizontal gene transfer – that would not have been discovered any other way,” said co-author Matt Kane, program director in the National Science Foundation’s (NSF) Division of Environmental Biology. “This finding extends our understanding of the role that this mechanism plays in evolution to eukaryotic microorganisms."
    • This quote is deeply troubling.  Genome sequencing did not reveal a new mechanism of evolution.  And it is thus also inaccurate to say 'it would not have been discovered any other way".  Lateral gene transfer was studies for many many many years before the first genome sequence was determined.  Certainly, comparative genome analysis helped reveal the extent of gene transfer but it is seriously inaccurate to say it "revealed a new mechanism of evolution".  Here for example is a link to a google search for the specific phrase "lateral gene transfer" in papers published prior to 1995.  And here is one for the phrase "horizontal gene transfer". 
    • I hoped that this was a misquote because the person quoted is Matt Kane - an NSF program officer responsible for many areas related to microbial studies.  But alas I found the press release from NSF with the same quote.  Perhaps NSF PR people misquoted Matt.  I hope they misquoted Matt.  Because if not - the quote grossly oversells genome sequencing and what has been learned from it and rather than standing on the shoulders of giants it makes the giants of the past seem like ants.  
  • "It's usually assumed that organisms with a nucleus cannot copy genes from different species--that's why eukaryotes depend on sex to recombine their genomes. "How has Galdieria managed to overcome this limitation? It's an exciting question. What Galdieria did is "a dream come true for biotechnology," says Weber."
    • This is wrong in so so many ways.  Again, as discussed above, eukaryotes have been known to undergo gene transfer for many years.  
    • And to say that the inability to acquire genes by LGT is why eukaryotes depend on sex to recombine their genes?  Really?  Uggh.  As far as I know there are no major theories out there that suggest sex is there because eukaryotes cannot undergo lateral transfer (although certainly some theories on the origin and maintenance of sex do indeed relate to increasing diversity by recombination).
    • And what makes this a dream come true for Biotech exactly? 
    • I note - this too was in the NSF press release.  Has NSF suddenly decided to become like NASA in terms of ludicrous PRs? 
I note - I do worry about the effect of calling out NSF on this in terms of my ability to get grants from them.  But this is just terrible stuff in this PR and story and it needs to be stopped.  I note further that I consider Matt Kane a friend and I hope that he clarifies his quote here and also manages to get NSF to be more rigorous in their PRs.


  1. Are these guys unaware of the endosymbiont hypothesis? How do they think has it come that genes encoding mitochondrial and plastide proteins are located in the nuclei of eukaryotes?

  2. This is indeed very troubling. At best it is ignorance of a huge body of work. At worst, willful misrepresentation. My friend Jack Heinemann would take issue with the lack of HGT to nucleated creatures, having clearly shown conjugation from E. coli to yeast in the 1980s. The Agrobacterium community should be equally upset. Josh Lederberg would be surprised to learn that HGT was discovered after the advent of comparative genomics.

  3. Is it common for program officers to be co-authors?

    1. That is mistake by the reporter. He is not a coauthor.


Irresponsible reporting on "poop doping" from the Washington Post

UPDATE - see below - the author updated her article including some of my critiques. Went on a bit of a Twitter tirade last night. See mor...