There are many discussions going on about a paper from Bordenstein and Theis that was published in PLOS Biology in August 2015. The paper is Bordenstein SR, Theis KR (2015) Host Biology in Light of the Microbiome: Ten Principles of Holobionts and Hologenomes. PLoS Biol 13(8): e1002226. doi:10.1371/journal.pbio.1002226
A few days ago a paper came out by Moran and Sloan that discussed an alternative view of Hologenomes: Moran NA, Sloan DB (2015) The Hologenome Concept: Helpful or Hollow? PLoS Biol 13(12): e1002311. doi:10.1371/journal.pbio.1002311.
I made some comments on Twitter when the 1st paper came out about how I was skeptical of the paper and in discussions with Seth Bordenstein I said I would try to write up my thoughts. And when I was pointed to the second paper today I posted to Twitter that I thought it was important and got into a brief discussion with Seth about the paper.
In thinking about the papers and science publishing and scientific discussions I have decicded to try and carry out a new experiment. I am going to go, as fast as I can, line for line through the papers and post my thoughts in response to those lines. And I will try to be honest even if my thoughts are not, well thought out or nice or helpful. I am just going to post the thoughts. And one reason I want to do this is I worry (or maybe realize) that my judgement may be being affected here by visceral responses to some of the lines. In particular, I confess, some of the way the Bordenstein and Theis article is written really rubs me the wrong way. Nothing personal against the authors. But the text did not agree with me in parts. And I think that may have affected my response to the article. I do not know for sure but it seems possible.
Regardless, I am going to try and go through this. And for now I am going to just start with the Abstract.
Groundbreaking research on the universality and diversity of microorganisms is now challenging the life sciences to upgrade fundamental theories that once seemed untouchable.I personally find this to be a bit too extreme. Really - did they once seem untouchable? To whom?
To fully appreciate the change that the field is now undergoing, one has to place the epochs and foundational principles of Darwin, Mendel, and the modern synthesis in light of the current advances that are enabling a new vision for the central importance of microbiology.I think it is overstating the "central importance of microbiology" to place it somehow in line with Darwin, Mendel and the modern synthesis
Animals and plants are no longer heralded as autonomous entities but rather as biomolecular networks composed of the host plus its associated microbes, i.e., "holobionts."While on the one hand I agree with part of this statement I think it is making a claim and stating it as a fact when this is what is being debated.
As such, their collective genomes forge a "hologenome," and models of animal and plant biology that do not account for these intergenomic associations are incomplete.
Certainly animal and plant biology has to account for microbes. But it is false logic to say that one can only account for microbes by following the hologenome concepts.
Here, we integrate these concepts into historical and contemporary visions of biology and summarize a predictive and refutable framework for their evaluation.No thoughts on this.
Specifically, we present ten principles that clarify and append what these concepts are and are not, explain how they both support and extend existing theory in the life sciences, and discuss their potential ramifications for the multifaceted approaches of zoology and botany.Confession. Saying ones own principles "clarify" something rubs me the wrong way. I would really have preferred it if they said "attempt to clarify".
We anticipate that the conceptual and evidence-based foundation provided in this essay will serve as a roadmap for hypothesis-driven, experimentally validated research on holobionts and their hologenomes, thereby catalyzing the continued fusion of biology's subdisciplines.I find this to be really overstated too. I don't think what you have presented in this paper is a roadmap. And for you to call it that sets up this essay as basically saying that everything else that has come before is limited and lame.
At a time when symbiotic microbes are recognized as fundamental to all aspects of animal and plant biology, the holobiont and hologenome concepts afford a holistic view of biological complexity that is consistent with the generally reductionist approaches of biology.I do not think symbiotic microbes are fundamental to all aspects of animal and plant biology. I think this is actually a silly statement and makes me doubt the objectivity of the authors.
UPDATE: See part 2 here.