A special special issue of RNA Biology – dedicated to Carl Woese and Open Access too

A must read for, well, everyone out there: RNA Biology: Table of Contents for a special issue dedicated to / about Carl Woese.  The issue includes an amazing collection of papers:

A special issue in memoriam of Carl Woese
Renée Schroeder
Page 169

Introduction to special Carl Woese issue in RNA Biology
Robin R Gutell
Pages 170 – 171

Carl Woese: A structural biologist’s perspective
Peter B Moore
Pages 172 – 174

Early days with Carl
Ralph Wolfe
Page 175

Molecular phylogenetics before sequences: Oligonucleotide catalogs as k-mer spectra
Mark A Ragan, Guillaume Bernard and Cheong Xin Chan
Pages 176 – 185

Constraint and opportunity in genome innovation
James A Shapiro
Pages 186 – 196

Carl Woese’s vision of cellular evolution and the domains of life
Eugene V Koonin
Pages 197 – 204

From Woese to Wired: The unexpected payoffs of basic research
Ann Reid
Pages 205 – 206

Carl Woese, Dick Young, and the roots of astrobiology
John D Rummel
Pages 207 – 209

Life is translation
Bojan Zagrovic
Pages 210 – 212

Organelle evolution, fragmented rRNAs, and Carl
Michael W Gray
Pages 213 – 216

Remembering Carl Woese
Kenneth R Luehrsen
Pages 217 – 219

Woese on the received view of evolution
Sahotra Sarkar
Pages 220 – 224

This article is open accessSecondary structure adventures with Carl Woese
Harry F Noller
Pages 225 – 231

A backward view from 16S rRNA to archaea to the universal tree of life to progenotes: Reminiscences of Carl Woese
Roger A Garrett
Pages 232 – 235

Carl Woese in Schenectady: The forgotten years
Larry Gold
Pages 236 – 238

History and impact of RDP: A legacy from Carl Woese to microbiology
James R Cole and James M Tiedje
Pages 239 – 243

Casting a long shadow in the classroom: An educator’s perspective of the contributions of Carl Woese
Mark Martin
Pages 244 – 247

Looking in the right direction: Carl Woese and evolutionary biology
Nigel Goldenfeld
Pages 248 – 253

Ten lessons with Carl Woese about RNA and comparative analysis
Robin R Gutell
Pages 254 – 272

Memories of Carl from an improbable friend
Harris A Lewin
Pages 273 – 278

Time for a Nobel Prize for the human microbiome? I think so … what do you think?

Well, previously I have written about how I thought that there should have been a Nobel Prize awarded  to Carl Woese and Norm Pace for pioneering work on microbial diversity.  See for example “Some arguments for why Carl Woese (and probably Norm Pace) deserves a Nobel Prize“.  Alas Carl Woese passed away recently and is no longer eligible.  However, in a way this opens up things to a perhaps more medical driven Nobel prize in Medicine for the microbiome.  I believe that the human microbiome has been shown to be important enough in medicine to be deserving of a Nobel Prize in medicine.

And if that is true, then we can ask “Are there any people who would deserve a prize in this area?”  And the answer is pretty clearly yes.  I would suggest that there are two people who deserve such a recognition: Norm Pace and Jeff Gordon.  Norm Pace for his pioneering work on characterizing microbes indirectly via sequencing their RNA and DNA, especially their ribosomal RNA genes.  And Jeffrey Gordon for his pioneering work on animal and the human micro biome and in showing that the microbiome plays fundamental roles in animals and human health and phenotypes.

I will write more about this later but just wanted to get this thought out there … and see what people think.

UPDATE September 2015 I note. I have been and continue to be concerned with the spread of “microbiomania” which is the term I use to refer to “Overselling the Microbiome“. Even though this still is a problem, I also believe the microbiome has now been clearly shown to be critically important to human health in diverse ways and I do think it is appropriate to award a Nobel Prize in this area.

Also note Reuters is reporting that Jeffrey Gordon is on their candidate list this year (based on ISI predictions).

Reading in detail Carl Woese’s 1998 "Manifesto on Microbial Genomics" for the first time …

I am a bit stunned by this paper from Carl Woese in 1998 which I was aware of but have not read in detail until now: ScienceDirect.com – Current Biology – A manifesto for microbial genomics

I re-discovered it because I am making a compilation of papers by Woese in relation to the tribute page I have set up.  And the title (a manifesto about microbial genomics) combined with the date (1998 – early in the genome sequencing era) struck me as something worth looking at.  Plus I knew others (e.g., Phil Hugenholtz, Nikos Kyrpides, …) had mentioned this paper to me so I figured – hey – how about actually reading it in detail.  And fortunately it is freely available at the Current Biology web site (not sure why that is actually).  Anyway – what I found in the paper is basically an argument for much of my career from 1998-2008.

Some choice lines in here but the crux is as follows

The first order of business in microbial genomics should be a phylogenetically representative genomic screen of the microbial world. In other words, all the major microbial taxa and their subdivisions — which are the major source of biological diversity on Earth — should be represented by several genome sequences. There are now more than 30 recognized major eubacterial taxa — each the phylogenetic equivalent of a eukaryotic kingdom — and at least half that number in the (far less well characterized) Archaea; not to mention the yet-to-be-discovered kingdoms among the unicellular eukaryotes.

This basically lays out the Tree of Life project I co-ran at TIGR and the Genomic Encyclopedia of Bacteria and Archaea project I co-ran / run at the DOE JGI.

The ending is perfect

This is not the place to go into the specifies of which microbial genomes would be most useful. I would suggest, however, that a phylogenetic tree hang on the wall of every laboratory in which microbial genomes are being sequenced — for inspiration.

Somehow I had missed the crux of this paper until now.  I think it is worth reading by everyone out there working on microbes and/or their genomes.

Oh – and here is the compilation of Woese’s papers I am making in Mendeley.


RIP Carl Woese: Collecting posts / notes / other information about my main science hero here

My tribute to Carl Woese 12/30/12

Sadly, Carl Woese has passed away.  I am collecting some links and posts about him here in his memory.  He was without a doubt the person who most influenced my career as a scientist.

News stories about Woese’s passing

Some of my posts about Woese

Woese Tree of Life pumpkin (by J. Eisen)

Storification of Tweets and other posts about his passing //storify.com/phylogenomics/rip-carl-woese.js?template=slideshow[View the story “RIP Carl Woese” on Storify]

Other posts worth reading about Woese’s passing

Some videos with Woese 


My graduate student Russell Neches used a laser to etch a picture of Carl Woese on a piece of toast.


2003 email from Carl Woese to Mitch Sogin after winning Crafoord Prize

I had posted an email here from Carl Woese to Mitch Sogin (with Mitch’s permission).  However, in retrospect I feel uncomfortable posting private emails of Carl Woese’s here as he is not around to give permission.  So I have removed them.  Apologies to all who may have felt uncomfortable about the posting and to those who wish it would remain public.  But I just do not feel comfortable with this anymore.

Best email I have ever received – from Carl Woese 10/29/2011

I had posted an email exchange here between Carl Woese and myself.  However, in retrospect I feel uncomfortable posting private emails of Carl Woese’s here as he is not around to give permission.  So I have removed them.  Apologies to all who may have felt uncomfortable about the posting and to those who wish it would remain public.  But I just do not feel comfortable with this anymore.

Email exchanges between Robin Gutell and Carl Woese

I had posted emails here between Carl Woese and Robin Gutell (with Robin’s permission).  However, in retrospect I feel uncomfortable posting private emails of Carl Woese’s here as he is not around to give permission.  So I have removed them.  Apologies to all who may have felt uncomfortable about the posting and to those who wish it would remain public.  But I just do not feel comfortable with this anymore.

Some arguments for why Carl Woese (and probably Norm Pace) deserves a Nobel Prize

Compiling posts and articles discussing why Carl Woese deserves a Nobel Prize.  Will be writing a new article on this but felt like I should share the articles in case I don’t get done in time

I note I do not think Woese should win a Nobel for discovering the archaea.  That was a groundbreaking finding but it does not fit well with the Nobel Prize categories.  I think he should win it for the concept of molecular classification of microorganisms and applying this in general to the microbial world around us.  This concept (expanded by Norm Pace and colleagues to uncultured microbes) revolutionized our approach to studying single microbes in the environment, to studying single microbes infecting people and to studying communities of microbes in and on people.  And thus Woese and Pace in my opinion deserve the Nobel Prize for Medicine.  I will be expanding on this in a future post …

Evolution pumpkins – from Darwin to Woese

OK I know I am a geek, but I do think these came out pretty well …

“I think” in honor of Darwin

Woese Tree of Life

Here’s hoping molecular classification/systematics of cultured & uncultured microbes wins #NobelPrize in medicine

From Wu et al. 2009. A phylogeny driven genomic encyclopedia of bacteria and archaea. Nature 462, 1056-1060 doi:10.1038/nature08656  http://bit.ly/8Y8xea

Well, I am always hopeful.  Every year when the Nobel Prizes come around I am alway hoping that one of them goes to someone involved in studying microbial diversity in some way.  And really, there is a potential Nobel Prize in Physiology or Medicine out there in this area.  Sure they do not give out a Nobel in biology, or evolution or ecology.  But I think a good argument could be made for giving out a Nobel Prize in Physiology or Medicine to those who have worked on molecular systematics of cultured and uncultured microbes.

Why should this attract the attention of those giving out the Nobel Prizes?  Well, without molecular systematics of microbes we would be completely lost in a sea of microbial diversity.  And with such molecular systematics we can not only make much more sense out of the biology of cultured organisms, but we can go to environments and determine who is out there by sampling their genes.  And this type of work has undoubtedly revolutionized medicine, from determining what antibiotics are most likely to be useful in infections, to tracking emerging infectious diseases, to studying the vast diversity of microbes we have not yet cultured in the lab.  Certainly with the growing importance of the human microbiome in medical studies and the growing application of molecular systematics (e.g., rRNA surveys) to all sorts of aspects of microbiology, the time is ripe for an award in this area.

And who would get an award if one was given.  Well, certainly one of the people should be Carl Woese, who pioneered the use of comparative analysis of the sequences of rRNA genes to the study of systematics of microbes.  Woese of course was responsible for proposing the existence of a third branch in the tree of life – the archaea.  And even if you do not personally believe that the “three domain” tree of life is perfectly correct, Woese and colleagues (e.g., George Fox, who was a coauthor on some of the pioneering papers) were responsible for making microbial systematics a much more rigorous science than it had been.

And I think a good argument could be made for including Norm Pace in this Nobel as he was the one mostly responsible for pushing the sequencing and analysis of rRNA genes for studying microbes in the environment (though I note, others like Mitch Sogin also helped pioneer this field).  There is a direct path from Woese through Pace to much of modern molecular studies of microbes in the environment, including the latest approach – metagenomics.  In fact, there has even been a Nobel Prize already given that depended on much of this work – the one in 2005 to Barry Marshall and Robin Warren for discovery of the role of Helicobacteri pylori in causing stomach ulcers.

Anyway – just a short post about this – maybe more later.  But I sincerely think this would be a well deserved area in which to hand out one of those Nobel Prizes.  Not holding my breath, but always hopeful.

Here some potentially related things that I have written that may be useful to read: