My personal thoughts on Bordenstein and Theis Holobiont Paper – part 2

See this The Tree of Life: My personal thoughts on Bordenstein and Theis: Host Biology in Light of the Microbiome: Ten Principles of Holobionts and Hologenomes for part 1 and background.  I note – part of why I wrote the previous post was Seth had complained in a blog post that some authors seemed to have not read his paper.  So I decided to read it.  And to comment on it publically.

After I posted about this there was some back and forth with Seth on Twitter.  Here is some of it:

Anyway, I am going through, sentence by sentence the paper.

I did the Abstract in the last post.  Now on to the Introduction

“The time has come to replace the purely reductionist ‘eyes-down’ molecular perspective with a new and genuinely holistic, eyes-up, view of the living world, one whose primary focus is on evolution, emergence, and biology’s innate complexity.”—Carl Woese (2004) [1]

Nice quote.

At the end of the 19th century, the theory of evolution via natural selection was birthed with the appreciation that individual animals and plants vary in their phenotypes and that competition at the individual level drives gradual change in the frequencies of these phenotypes [2]. 

No comments.

From this early vantage point, fusing evolution with Mendelian genetics in the early 20th century was a seamless transition in biology, namely one based on the framework that phenotypes in the individual animal and plant are encoded by the nuclear genome under the laws of Mendelian inheritance [3–5].

I really do not feel comfortable calling this a seamless transition.  From my reading and what I know of the history, it took a lot of work by people to both figure out how to make this transition, how to refine it and then how to convince others that it was correct.

In the mid-20th century, the modern synthesis grounded the nucleocentric foundation of zoology and botany in three areas: (1) the nuclear mutability and recombinogenic nature of organisms, (2) the sorting of this genetic variation by natural selection, and (3) the observations that macroevolutionary processes such as the origin of species can be explained in a manner that aligns with Mendelian genetics and microevolutionary mechanisms [6].

Calling zoology and botany “nucleocentric” seems unnecessary to me although I guess I am not sure what they point of this is.

The foundation of the modern synthesis remains as scientifically sound today as when it was conceived. 

I am not sure I understand what this is saying.  How would the scientific soundness of the synthesis change over time?  Or do they mean here “the perception of the scientific soundness?”

However, it is critical to recognize that microbiology was largely divorced from these early epochs in the life sciences.


The modern synthesis commenced at a time when the germ theory of disease dictated the prevailing wisdom on microbes, and the molecular tools used to understand the microbial world and its influence were inferior to those available now [7–11].

This is true but the tools were also inferior for characterizing anything.  Plus I do not think it was the molecular tools per se that changed things.  It was also ideas and theories.

The theories of gradual evolution and the modern synthesis were thus forged during periods of eukaryocentricism and nucleocentrism that did not appreciate the centrality of microbiology in zoology and botany because of limitations in perspective and technology.

Yes, good to mention the “limitations in perspective”.  But I am not sure what eukaryocentrism is exactly.  Or what nucleocentrism is either.  And I just do not feel comfortable with the “centrality of microbiology in zoology and botany statement”.  This seems to be putting the cart before the horse.  Are they central?  I don’t actual know.  Are they important?  Absolutely.  That is why I study host-microbe interactions.  But are they “central” – I would not go that far.  And I thought part of the point of this was that we need to test that, not posit it.

Today, there is an unmistakable transformation happening in the way that life is comprehended [12–16], and it is as significant for many biologists as the modern synthesis. Animals and plants are no longer viewed as autonomous entities, but rather as “holobionts” [17–21], composed of the host plus all of its symbiotic microbes (definitions in Box 1). 

I find this to be an enormous overstatement.  I for one do not believe we are even remotely near a point where understanding that plants and animals are “not autonomous entities” is getting to something akin to the modern synthesis.

The term “holobiont” traces back to Lynn Margulis and refers to symbiotic associations throughout a significant portion of an organism’s lifetime, with the prefix holo- derived from the Greek word holos, meaning whole or entire. 

I was not aware of the history.

Amid the flourishing of host microbiome studies, holobiont is now generally used to mean every macrobe and its numerous microbial associates [19,22], and the term importantly fills the gap in what to call such assemblages. 

I am not so sure that this is a useful term and I am not convinced that it “importantly” fills any gap.  Whether it fills any gap depends entirely on whether many of the claims in this paper are supported by evidence.  So stating this in the introduction seems awkward.

Symbiotic microbes are fundamental to nearly every aspect of host form, function, and fitness, including in traits that once seemed intangible to microbiology: behavior [23–26], sociality [27–30], and the origin of species [31]. 

I agree that microbes play more of a role than was thought.  I don’t think they play fundamental roles in “nearly every aspect of host form, function and fitness.”  What about vision? Xylem formation? Meiosis? Speech? Muscle contraction? Flight mechanics? And 100,000 other things.  Sure, microbes play fundamental roles in many aspects of host biology.  And that is awesome and why I study host-microbe interactions.  But this “nearly every aspect” is just really way overboard.

The conviction for a central role of microbiology in the life sciences has been growing exponentially, and microbial symbiosis is advancing from a subdiscipline to a central branch of knowledge in the life sciences [14,32–35].

I don’t find this convincing.

This revelation brings forth several newly appreciated facets of the life sciences, including the testable derivation that the nuclear genome, organelles, and microbiome of holobionts comprise a hologenome [35–37]. 

Ok.  This I am OK with.  Because rather than overstating things this presents something, finally, as something to test.

The hologenome concept is a holistic view of genetics in which animals and plants are polygenomic entities. Thus, variation in the hologenome can lead to variation in phenotypes upon which natural selection or genetic drift can operate. 

This seems to be presenting material as fact rather than hypothesis.

While there is a rich literature on coevolutionary genomics of binary host–microbe interactions, there have been few systematic attempts to align the true complexity of the total microbiome with the modern synthesis in a way that integrates these disparate fields [38–40].

I generally agree with this.

The object of this essay is to make the holobiont and hologenome concepts widely known. We clarify and append what they are and are not, explain how they are both consistent with and extend existing theory in ecology and evolutionary biology, and provide a predictive framework for evaluating them.


Our goal is to provide the main conceptual foundation for future hypothesis-driven research that unifies perceived divisions among subdisciplines of biology (e.g., zoology, botany, and microbiology) and advances the postmodern synthesis that we are now experiencing [41,42]. 

This rubs me the wrong way.  To aim to “provide the main conceptual foundation” seems to be exceptionally bold and arrogant.  And to, in this one paper provide such a conceptual foundation – I don’t think so.  And then to advance the post modern synthesis too?  How about we judge that AFTER the article is published not before?

We distill this topic with evidence-based reasoning to present the ten principles of holobionts and hologenomes (summarized in Box 1).

I guess I don’t really like this either.  “The” 10 principles?  How about just “10 principles”.  As this is written it implies there are no other principles that could be hypothesized.

OK … so that is the Introduction.  Will try to continue with the meat of the paper soon.

UPDATE: See part 3 here.

My personal thoughts on Bordenstein and Theis: Host Biology in Light of the Microbiome: Ten Principles of Holobionts and Hologenomes.

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.

Some new preprints of interest and comments on "The case for preprints in biology"

Getting more and more into preprints (see for example these posts Guest post from Jake Scott: Building trust: a sine qua non for successful acceptance of preprints in the biological sciences and More bio preprint discussion sites …).  So am starting to browse preprint servers a bit more and I have found some recently posted preprints of interest:

From arVix:

From PeerJ preprints

I wondered – where else might one find Biology themed preprints.  And a little google searching let me to this new PLOS Biology paper which somehow I had missed a few weeks ago: The Case for Open Preprints in Biology
(Full citation: Desjardins-Proulx P, White EP, Adamson JJ, Ram K, Poisot T, et al. (2013) The Case for Open Preprints in Biology. PLoS Biol 11(5): e1001563. doi:10.1371/journal.pbio.1001563)
Wow – how perfect.  In their paper they not only lay out the case for why preprints would be a good thing in biology but discuss some of the options.  And in addition to PeerJ and arXiv they point to Figshare, Github, and ResearchGate.
Below is Figure 1 from their paper:
Figure 1. It can take several months before a submitted paper is officially published and citable.. Meanwhile, few people are aware of the research that has been done since, typically, only close colleagues are given access to the preprints. With public preprint servers, the science is immediately available and can be openly discussed, analyzed, and integrated into current research. doi:10.1371/journal.pbio.1001563.g001
They also show that in arXiv submissions in the qBio section are going up but not nearly as much as submissions in other fields
Figure 2. Submissions to the quantitative biology section lag behind physics, mathematics, and computer science.  Data from [19]. doi:10.1371/journal.pbio.1001563.g002.  The reference to 19 is to Warner S (2012) Data for arXiv submissions by subject and year. Available:​966. Accessed 14 April 2013.
I think this paper is worth a look for anyone interest in scientific publishing.  I like their last line and will end my post with it:

Preprints are simply bypassing this model for what we believe is the progress of science: they speed up the dissemination of scientific discoveries and put on readers’ shoulders the responsibility to judge originality and pertinence.

The gurus of evolution predict the future #PLOSBiology

Nice commentary / viewpoint piece in PLOS Biology last months: PLOS Biology: Evolutionary Biology for the 21st Century

Citation.Jonathan Losos, Stevan J. Arnold, Gill Bejerano, E. D. Brodie III, David Hibbett, Hopi E. Hoekstra, David P. Mindell, Antónia Monteiro, Craig Moritz, H. Allen Orr, Dmitri A. Petrov, Susanne S. Renner, Robert E. Ricklefs, Pamela S. Soltis, Thomas L. Turner (2013) Evolutionary Biology for the 21st Century. PLoS Biol 11(1): e1001466. doi:10.1371/journal.pbio.1001466

They discuss issues like Biodiversity Informatics (see Figure to the left) and evolutionary applications like evolutionary medicine, food production, sustaining biodiversity, computational algorithms, and justice.  They also discuss issues like the oncoming onslaught of specimens and the need to link up with museums who have expertise in dealing with such issues.  Anyway – it is worth a look.  Not the most visionary of pieces ever but it has some concrete suggestions and predictions that will be of use.

Crosspost from PLOS Biologue: Working to increase diversity of PLOS Biology Academic Editors and Advisory Board members

On the PLOS Biologue (the blog for PLOS Biology) I have a post that may be of interest.  I discuss our efforts to increase the diversity of the people involved in the various Boards of PLOS Biology.  This is my first task I have taken as the Chair of the PLOS Biology Advisory Board.  See the post: Working to increase diversity of PLOS Biology Academic Editors and Advisory Board members.

Go PLOS Biology – getting lots of press coverage for recent pubs

Just got this email from PLoS Biology and thought I would share – it has links to press coverage of recent PLoS Bio papers  :

We are writing to update you on some papers recently published in PLoS Biology.This is a summary of our recent media coverage for PLoS Biology board members, friends, and for editors. Thank you again for your support of the journal.

On January 3, PLoS Biology published an article by Prof. Alex Rogers et al., which detailed a survey of Antarctic waters along the East Scotia Ridge in the Southern Ocean, revealing a new vent biogeographic province among previously uncharacterized deep-sea hydrothermal vent communities. This received significant coverage in the media, a selection of which is below:

The New York Times
The Guardian
Washington Post

PBS News Hour (video)
BBC World Service (audio)
Press Association
Discovery News
Reuters (video)
The Telegraph
Scientific American
National Geographic
ABC (Australia)
Sydney Morning Herald
CBC (Canada)
Fox News
New Scientist
The Mirror
The Daily Mail
Indian Express

In the same issue, PLoS Biology published an article by Dr David Ornitz and colleagues, which described how FGF20 signaling in mice is required specifically for the differentiation of cochlear outer hair cells – the cells most often damaged during age-related hearing loss. This also received attention in the media, including the following:

NHS Choices
Press Association
The Mirror
The Daily Mail
Irish Examiner

What is a nice chloroplast like you doing in a parasite like that?

Cool new paper from Joe Derisi’s lab: PLoS Biology: Chemical Rescue of Malaria Parasites Lacking an Apicoplast Defines Organelle Function in Blood-Stage Plasmodium falciparum. by Ellen Yeh and Joseph L. DeRisi. doi: 10.1371/journal.pbio.1001138

In it they use some experimental techniques to try and track down the elusive function of the apicoplast in Plasmodium falciparum, the causative agent of malaria.  The apicoplast is an organelle that is evolutionarily derived from chloroplasts (and thus derived originally from cyanobacteria).  Due to it’s cyanobacterial origins many have thought that it might serve as a good target for drugs to try and kill Plasmodium species because in theory such drugs if specific should not have significant detrimental effects on hosts like humans due to our lack of known important cyanobacterial associates.

Here is their abstract:

Plasmodium spp parasites harbor an unusual plastid organelle called the apicoplast. Due to its prokaryotic origin and essential function, the apicoplast is a key target for development of new anti-malarials. Over 500 proteins are predicted to localize to this organelle and several prokaryotic biochemical pathways have been annotated, yet the essential role of the apicoplast during human infection remains a mystery. Previous work showed that treatment with fosmidomycin, an inhibitor of non-mevalonate isoprenoid precursor biosynthesis in the apicoplast, inhibits the growth of blood-stage P. falciparum. Herein, we demonstrate that fosmidomycin inhibition can be chemically rescued by supplementation with isopentenyl pyrophosphate (IPP), the pathway product. Surprisingly, IPP supplementation also completely reverses death following treatment with antibiotics that cause loss of the apicoplast. We show that antibiotic-treated parasites rescued with IPP over multiple cycles specifically lose their apicoplast genome and fail to process or localize organelle proteins, rendering them functionally apicoplast-minus. Despite the loss of this essential organelle, these apicoplast-minus auxotrophs can be grown indefinitely in asexual blood stage culture but are entirely dependent on exogenous IPP for survival. These findings indicate that isoprenoid precursor biosynthesis is the only essential function of the apicoplast during blood-stage growth. Moreover, apicoplast-minus P. falciparum strains will be a powerful tool for further investigation of apicoplast biology as well as drug and vaccine development.

The author summary is a bit nicer in my opinion:

Malaria caused by Plasmodium spp parasites is a profound human health problem that has shaped our evolutionary past and continues to influence modern day with a disease burden that disproportionately affects the world’s poorest and youngest. New anti-malarials are desperately needed in the face of existing or emerging drug resistance to available therapies, while an effective vaccine remains elusive. A plastid organelle, the apicoplast, has been hailed as Plasmodium’s “Achilles’ heel” because it contains bacteria-derived pathways that have no counterpart in the human host and therefore may be ideal drug targets. However, more than a decade after its discovery, the essential functions of the apicoplast remain a mystery, and without a specific pathway or function to target, development of drugs against the apicoplast has been stymied. In this study, we use a simple chemical method to generate parasites that have lost their apicoplast, normally a deadly event, but which survive—“rescued” by the addition of an essential metabolite to the culture. This chemical rescue demonstrates that the apicoplast serves only a single essential function, namely isoprenoid precursor biosynthesis during blood-stage growth, validating this metabolic function as a viable drug target. Moreover, the apicoplast-minus Plasmodium strains generated in this study will be a powerful tool for identifying apicoplast-targeted drugs and as a potential vaccine strain with significant advantages over current vaccine technologies.

Also see their press release here.

Basically they are trying to use various experimental tricks to figure out which functions of the apicoplast are essential.  Many theories have been proposed over the years as to what the apicoplast is doing.  But few have gained significant evidence.  This paper is an important contribution because it suggests that one pathway in particular is most functionally important: the isopentenyl pyrophosphate (IPP) synthesis pathway.  See their model below:

Figure 5. Model of apicoplast function.
(Top) The essential function of the apicoplast is the production of isoprenoid precursors, IPP and DMAPP, which are exported into the cytoplasm and used to synthesize small molecule isoprenoids and prenylated proteins. Parasites that are unable to synthesize isoprenoid precursors either due to inhibition of the biosynthetic pathway by fosmidomycin or loss of the apicoplast following doxycycline inhibition can be chemically rescued by addition of exogenous IPP (red). The exogenous IPP enters the host cell through unknown membrane transporters and fulfills the missing biosynthetic function. (Bottom) Reaction scheme for MEP pathway biosynthesis of IPP and DMAPP with the enzymatic step inhibited by fosmidomycin indicated.

Anyway – I have always been fascinated by apicoplasts because they are so weird.  They reflect a strange evolutionary history of Apicomplexans in that this is a eukaryotic lineage that at some point brought into itself an entire photosynthetic algal cell as a symbiont.  And for reasons still unknown (if there are reasons …) the chloroplast of the algal symbiont was retained while most of the rest of the symbiont was ditched.  So that the resulting cells looked something like this:


Evolution is indeed very weird.  And once it was discovered that the apicoplast was in fact derived from chloroplasts (this was discovered using molecular phylogenetics) (e.g., see people have been wondering if it might make a good drug target.  But people have also been wondering – what do Apicomplexans do with a chloroplast like organelle when they do not photosynthesize.  So the Derisi paper is interesting both from a drug treatment point of view but also from an evolution point of view.

Anyway – here are some other links worth looking at:

Bacteria & archaea don’t get no respect from interesting but flawed #PLoSBio paper on # of species on the planet

Uggh. Double uggh. No no. My first blog quadruple uggh. There is an interesting new paper in PLoS Biology published today. Entitled “How many Species Are There on Earth and in the Ocean?” PLoS Biol 9(8): e1001127 – it is by Camilo Mora, Derek Tittensor, Sina Adl, Alastair Simpson and Boris Worm. It is accompanied by a commentary by none other than Robert May, one of the greatest Ecologists of all time: PLoS Biology: Why Worry about How Many Species and Their Loss?

I note – I found out about this paper from Carl Zimmer who asked me if I had any comments.  Boy did I.  And Zimmer has a New York Times article today discussing the paper: How Many Species on Earth? It’s Tricky.  Here are my thoughts that I wrote down without seeing Carl’s article, which I will look at in a minute.

The new paper takes a novel approach to estimating the number of species. I would summarize it but May does a pretty good job:
“Mora et al. [4] offer an interesting new approach to estimating the total number of distinct eukaryotic species alive on earth today. They begin with an excellent survey of the wide variety of previous estimates, which give a range of different numbers in the broad interval 3 to 100 million species”
“Mora et al.’s imaginative new approach begins by looking at the hierarchy of taxonomic categories, from the details of species and genera, through orders and classes, to phyla and kingdoms. They documented the fact that for eukaryotes, the higher taxonomic categories are “much more completely described than lower levels”, which in retrospect is perhaps not surprising. They also show that, within well-known taxonomic groups, the relative numbers of species assigned to phylum, class, order, family, genus, and species follow consistent patterns. If one assumes these predictable patterns also hold for less well-studied groups, the more secure information about phyla and class can be used to estimate the total number of distinct species within a given group.”
The approach is novel and shows what appears to be some promise and robustness for certain multicellular eukaryotes. For example, analysis of animals shows a reasonable leveling off for many taxonomic levels:

Figure 1. Predicting the global number of species in Animalia from their higher taxonomy. (A–F) The temporal accumulation of taxa (black lines) and the frequency of the multimodel fits to all starting years selected (graded colors). The horizontal dashed lines indicate the consensus asymptotic number of taxa, and the horizontal grey area its consensus standard error. (G) Relationship between the consensus asymptotic number of higher taxa and the numerical hierarchy of each taxonomic rank. Black circles represent the consensus asymptotes, green circles the catalogued number of taxa, and the box at the species level indicates the 95% confidence interval around the predicted number of species (see Materials and Methods).
From Mora C, Tittensor DP, Adl S, Simpson AGB, Worm B (2011) How Many Species Are There on Earth and in the Ocean? PLoS Biol 9(8): e1001127. doi:10.1371/journal.pbio.1001127

They also do a decent job of testing their use of higher taxon discovery to estimate number of species.  Figure 2 shows this pretty well.

Figure 2. Validating the higher taxon approach. We compared the number of species estimated from the higher taxon approach implemented here to the known number of species in relatively well-studied taxonomic groups as derived from published sources [37]. We also used estimations from multimodel averaging from species accumulation curves for taxa with near-complete inventories. Vertical lines indicate the range of variation in the number of species from different sources. The dotted line indicates the 1∶1 ratio. Note that published species numbers (y-axis values) are mostly derived from expert approximations for well-known groups; hence there is a possibility that those estimates are subject to biases arising from synonyms.

So all seems hunky dory and pretty interesting.  That is, until we get to the bacteria and archaea.  For example, check out Table 2:

Table 2. Currently catalogued and predicted total number of species on Earth and in the ocean.

Their approach leads to an estimate of 455 ± 160 Archaea on Earth and 1 in the ocean.  Yes, one in the ocean.  Amazing.  Completely silly too.  Bacteria are a little better.  An estimate of 9,680 ± 3,470 on Earth and 1,,320 ±436 in the oceans.  Still completely silly.

Now the authors do admit to some challenges with bacteria and archaea. For example:

We also applied the approach to prokaryotes; unfortunately, the steady pace of description of taxa at all taxonomic ranks precluded the calculation of asymptotes for higher taxa (Figure S1). Thus, we used raw numbers of higher taxa (rather than asymptotic estimates) for prokaryotes, and as such our estimates represent only lower bounds on the diversity in this group. Our approach predicted a lower bound of ~10,100 species of prokaryotes, of which ~1,320 are marine. It is important to note that for prokaryotes, the species concept tolerates a much higher degree of genetic dissimilarity than in most eukaryotes [26],[27]; additionally, due to horizontal gene transfers among phylogenetic clades, species take longer to isolate in prokaryotes than in eukaryotes, and thus the former species are much older than the latter [26],[27]; as a result the number of described species of prokaryotes is small (only ~10,000 species are currently accepted).

But this is not remotely good enough from my point of view. Their estimates of ~ 10,000 or so bacteria and archaea on the planet are so completely out of touch in my opinion that this calls into question the validity of their method for bacteria and archaea at all. 
Now you may ask – why do I think this is out of touch. Well because reasonable estimates are more on the order or millions or hundreds of millions, not tens of thousands. To help people feel their way through the literature on this I have created a Mendeley group where I am posting some references worth checking out.

I think it is definitely worth looking at those papers.  But just for the record, some quotes might be useful.  For example, Dan Dykhuizen writes

we estimate that there are about 20,000 common species and 500,000 rare species in a small quantity of soil or about a half million species.

And Curtis et al write:

We are also able to speculate about diversity at a larger scale, thus the entire bacterial diversity of the sea may be unlikely to exceed 2 × 10^6, while a ton of soil could contain 4 × 10^6 different taxa.

Are their estimates perfect?  No surely not.  But I think without a doubt the number of bacterial and archaeal species on the planet is in the range of millions upon millions upon millions.  10,000 is clearly not even close.  Sure, we do not all agree on what a bacterial or archaeal species is.  But with just about ANY definition I have heard, I think we would still count millions.

Given how horribly horribly off their estimates are for bacteria and archaea, I think it would have been better to be more explicit in admitting that their method probably simply does not work for such taxa right now.  Instead, they took the approach of saying this is a “lower bound”.  Sure.  That is one way of dealing with this.  But that is like saying “Dinosaurs lived at least 500 years ago” or “There are at least 10 people living in New York City” or “Hiking the Appalachian Trail will take at least two days.”  Lower bounds are only useful when they provide some new insight.  This lower bound did not provide any.
Mind you, I like the paper.  The parts on eukaryotes seem quite novel and useful.  But the parts of bacteria and archaea are painful.  Really really painful.
Mora, C., Tittensor, D., Adl, S., Simpson, A., & Worm, B. (2011). How Many Species Are There on Earth and in the Ocean? PLoS Biology, 9 (8) DOI: 10.1371/journal.pbio.1001127

I get complaints; and I want more (plus other comments) about #PLoS Biology

Many out there may know that I have a nice lofty title at PLoS Biology. I am the Academic Editor in Chief there. With this title I get a lot of complaints about PLoS Biology.

Alas, despite my lofty title, I do not actually run PLoS Biology. You see, PLoS Biology is a hybrid journal with both Professional editors and Academic Editors. The way it actually works is that the Professional Editors, under the direction of Theo Bloom, run the journal. As part of their running of the journal, they consult with Academic Editors (AEs) to get help in deciding if papers should be reviewed; if they are reviewed the AEs help suggest reviewers; and once reviews are back the AEs help in making decisions about the fate of the papers. They also consult AEs about a variety of other topics.

In the end, you could view the AEs, including the AEIC (that is, me) – as having an advisory role at PLoS Biology. Generally, decisions are made in a collaborative manner with the AEs but in the end, it is the professionals who make the “final” decisions regarding the journal. But they do listen when I tell them about what the community likes and dislikes about PLoS Biology.

Anyway, the reason I am writing is that in two weeks there is a meeting in San Francisco of the EICs of the various PLoS Journals and I will be going to this meeting. So here is my request:


What do you like?
What do you not like?
What new things would you like to see?
What would you like to get rid of?

Please either post your comments here, on twitter, or friendfeed or wherever. Or send them to me by email. And I will try to communicate them to the powers that be …

One of my new favorite things: paleovirology

Just a quick post here about a paper that came out about a month or so ago: PLoS Biology: Genomic Fossils Calibrate the Long-Term Evolution of Hepadnaviruses

This paper, by Clément Gilbert, Cédric Feschotte is quite cool.  In it they describe their work on “Paleovirology” where they look for viruses than have “endogenized” by inserting into the genome of some host species.  This endogenization is important in particular when the endogenous form becomes inactive and thus, in essence, trapped in the genome.  This in turn is important because many viruses evolve so rapidly when they are “free” that it is very hard to reconstruct their ancient history through comparative analysis.  But the endogenized viruses serve in essence as a molecular “fossil record” that aids in the comparison and phylogenetic analysis of various families of viruses.  As we get more and more genomes, this searching for and analysis of endogenous viruses will get much better.

Anyway, in the paper they report on endogenous viruses in the Zebra Finch genome that are in the Hepadnaviridae family.  Here is their summary:

Paleovirology is the study of ancient viruses and the way they have shaped the innate immune system of their hosts over millions of years. One way to reconstruct the deep evolution of viruses is to search for viral sequences “fossilized” at different evolutionary time points in the genome of their hosts. Besides retroviruses, few virus families are known to have deposited molecular relics in their host’s genomes. Here we report on the discovery of multiple fragments of viruses belonging to the Hepadnaviridae family (which includes the human hepatitis B viruses) fossilized in the genome of the zebra finch. We show that some of these fragments infiltrated the germline genome of passerine birds more than 19 million years ago, which implies that hepadnaviruses are much older than previously thought. Based on this age, we can infer a long-term avian hepadnavirus substitution rate, which is a 1,000-fold slower than all short-term substitution rates calculated based on extant hepadnavirus sequences. These results call for a reevaluation of the long-term evolution of Hepadnaviridae, and indicate that some exogenous hepadnaviruses may still be circulating today in various passerine birds.

Figure 4. Summary of the evolutionary scenario inferred in this study.

It is an interesting paper and worth a look if for those who have any interest in viral evolution. And I am becoming more and more fascinated by “Paleovirology” these days so I thought I would just post about this article here.  And I guess I am not alone in this opinion that the article is interesting (though I am late).  Here is some coverage of their paper:

Gilbert, C., & Feschotte, C. (2010). Genomic Fossils Calibrate the Long-Term Evolution of Hepadnaviruses PLoS Biology, 8 (9) DOI: 10.1371/journal.pbio.1000495