Monday, December 31, 2012

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

Other posts worth reading about Woese's passing
Some videos with Woese 







Miscellaneous

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

Sunday, December 30, 2012

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.

Wednesday, December 26, 2012

Microbial art for the holidays from the J. Craig Venter Institute

Saw this Tweet on Christmas Day
It was from Russell Neches, a PhD student in my lab.

Went to the site "La boite verte" and checked out their post "Des champignons de Noël."

Discovered it was based on a post from none other than the J. Craig Venter Institute's blog: Holiday Art" JCVI Blog. The post is by Stephanie Mounaud from December 2010 and it has three wonderful fungal art forms. I am embedding the images of them below:

Fungal Christmas Tree

Fungal Snowman


Fungal Christmas Tree2

Enjoy.

Wednesday, December 19, 2012

Great ideas in this #PLoSOne paper; except we published same idea 12 fu$*# years ago

Figure 1 from Pollock et al. 2000
Wow. I mean, imitation is a form of flattery. But this paper ... Grrrrrrr PLOS ONE: Conveniently Pre-Tagged and Pre-Packaged: Extended Molecular Identification and Metagenomics Using Complete Metazoan Mitochondrial Genomes In the paper the authors basically argue that for many purposes, including phylogenetic studies in particular, one could obtain many mitochondrial genomes at once by just pooling together samples from different organisms, shotgun sequencing the samples, and assembling the separate mitochondrial genomes out.  All one would need to do is to make sure the organisms pooled were distantly related enough such that their mitochondrial sequences would not cross assemble with each other.  They say things like:
We propose a novel approach for the isolation and sequencing of a universal, useful and popular marker across distant, non-model metazoans: the complete mitochondrial genome. It relies on the properties of metazoan mitogenomes for enrichment, on careful choice of the organisms to multiplex, as well as on the wide collection of accumulated mitochondrial reference datasets for post-sequencing sorting and identification instead of individual tagging. Multiple divergent organisms can be sequenced simultaneously, and their complete mitogenome obtained at a very low cost. We provide in silico testing of dataset assembly for a selected set of example datasets.
AND
We describe here the approach, the type of sequence data it generates, the procedure to recover mitochondrial genomes without external tagging, and some potential uses. We perform an in-silico validation test based on the analysis of a simulated dataset with read lengths of two different sizes to represent average read length of three 2nd generation desktop sequencing platforms, Illumina Mi-Seq, 454 GS junior and Ion Torrent PGM. Thus we can contrast their relative efficiencies for the experimental protocol proposed here.
Sounds great. Except I wrote a paper with David Pollock, Norman Doggett, and Michael Cummings published in 2000 proposing the same thing. Our paper:  Pollock DD, Eisen JA, Doggett NA, Cummings MP. Mol Biol Evol. 2000 Dec;17(12):1776-88. A case for evolutionary genomics and the comprehensive examination of sequence biodiversity.

Sampling the Wild Microbial Life of My Home

Just finally got around to doing the sampling of my house for the Wild Life of Our Homes microbial sampling project.

I signed up online, got a kit, got a registration code, and did the sampling today.  I swabbed the exterior door frame, an interior door frame, the kitchen counter and my pillow case.  Plus as a bonus, my 7 year old daughter helped - learning a bit about microbial sampling and also taking pictures of me at work (and a few of herself).




So many cool Citizen Microbiology projects going on now. Some information about them is here but I need to update the links there.

Tuesday, December 18, 2012

New "microbiology blog of the day" series at microBEnet


I am starting a new "microbiology blog of the day" series at the "microbiology of the built environment network (microBEnet)" site I co-run.  This is a culmination of something I started at the ASM Meeting in June.  When I went to the Communications Committee meeting, I suggested that there were lots of interesting microbiology blogs that ASM could do a better job of featuring.  I was asked "how many are there?"  And I said "there are dozens, and probably over 100".  A certain person on the committee who works on the current ASM blog expressed doubt that there were "more than five that are any good." I said I could compile a list easily.  And so I did this while at the ASM meeting.  And, well, I have been compiling ever since.  And the list grows and grows.

There are so many good microbiology - themed blogs out there that we created a compilation at microBEnet with the latest posts from each.  And at the suggestion of Nick Loman we pointed people to the OMPL file of the entire list which people can use to add the whole list to ones RSS reader.

So far I have written three simple summaries of blogs and will continue as long as I can ....  The first three are:
If you want to keep up with the posts, you need to subscribe to the microBEnet blog feed.  

There are so many great microbiology bloggers out there.  If you know of others not on our list, please let me know.

UPDATE 12/26 More Blogs Added to the Series

Sunday, December 16, 2012

Welcome to the Microbial Earth Project

Map of type strains.
All interested in microbes and their genomes should check out The Microbial Earth Project.  It "is an international effort to generate a comprehensive catalog from genome sequences of all the archaeal and bacterial type strains. The name of the project comes from the recognition that Earth is a predominantly a microbial planet, and by effect in order to understand life on our planet, we need to understand how microbial life works."

There are some 10,000 described type strains of bacteria and archaea.  Not really a lot given that there are probably millions upon millions of species of bacteria and archaea.  But it is what we have available to us in terms of the formally described and accepted species for which there is an available cultured strain.

At this site you can do things like "Adopt a Type Strain" or view a cool "Map of the type strains".

The Steering Committee for the project is


Much of the real work being done by Nikos Kyrpides, George Garrity, and others though I am very pleased to be a member of the Steering Committee.   One of my key jobs will be to get the word out early and often.  Hence this post.

Saturday, December 15, 2012

Not the best microbiology reporting: New Scientist on Lonely Bacterium

Too traumatized by the events in Connecticut to write much here but trying to focus on work for but so here goes.

Uggh. This article does not sit well with me: World's loneliest bug turns up in Death Valley - life - 13 December 2012 - New Scientist

The parts of the article I don't like?
  • "Uniquely, the bacterium has evolved to do without the sun's energy, relying only on hydrogen and sulphate, which can form naturally in its subterranean home." Umm ... how is this unique? What about all the other chemoautotrophic microbes known? What about deep sea vent communities? WTF this claim is so completely wrong I don't know what to say.
  • The article implies that one can use percent identity of the DNA of microbes to tell us how recently they shared a common ancestor. Hmm ... Is that under the model of "all organisms evolve in exactly the same way"? 
  • "Until recently, biologists thought that the species was confined to South Africa's depths". Really? So - the organism was discovered in one place and therefore we the biologists thought that it was confined there? 
  • Title: "World's loneliest bug turns up in Death Valley".  Sure - in the one system in South Africa this did seem to be a relatively lonely organism.  But to presume that this was the only place the organism was found was just silly. 
There.  Alas, writing this did not make me feel any better.  But it did distract me for a bit

Wednesday, December 12, 2012

Story behind the paper: Corey Nislow on Haloferax Chromatin and eLife

This is fun.  Today I am posting this guest post from Corey Nislow in my continuing "Story behind the paper" series.  The history of this post is what is most fun for me.  A few weeks ago I received this email from Corey:
Hi Jonathan, I hope this mail finds you well.
I wanted to alert you to a study from our lab that will be coming out in the inaugural issue of eLIFE.
After reading your PLoS ONE paper on the Haloferax volcanii genome (inspiration #1) I ordered the critter, prepared nucleosomes and RNA and we went mapping. Without a student to burden, I actually had to do some work...
Anyhow, we found that the genome-wide pattern of nucleosome occupancy and its relation to gene expression was remarkably yeast like. Unsure of where to send the story, we rolled the dice with the new open access journal eLIFE (inspiration #2) and the experience was awesome. I'm quite keen to pursue generating a barcoded deletion set for Hfx.
here's the paper (coming out Dec. 10) if you're curious.

And a PDF of the paper was attached.

And I wrote back quickly in my typically elegant manner:
completely awesome
But then I thought better of it and wrote again
So - can I con you into writing a guest post for my blog about the story behind this paper?  Or if you are writing a description somewhere else I would love to share it
And he said, well, yes.  And with a little back and forth, he wrote up the post that it below.  Go halophiles.  Go Haloferax.  Go open access.  Go science.


Chromatin is an ancient innovation conserved between Archaea and Eukarya  - The story behind the story

By Corey Nislow

My group first became interested in understanding the global organization of chromatin in early 2005 when Lars Steinmetz (now program leader at the EMBL) led a team effort at the Stanford Genome Center to design a state-of-the-art whole genome tiling microarray for Saccharomyces cerevisiae. These were heady times at Ron Davis’ Genome Technology shop and the array was another triumph of technology and teamwork. The array has over 7 million exceedingly small (5 µm²). The history of how this microarray transformed our understanding of the transcriptome began in 2006. As Lars’ group dug deeper, the extent of antisense transcription and its role in the regulation of expression became clear.

The availability of this array and its potential for asking interesting questions inspired me to convince William Lee, a new graduate student in my group (now at Memorial Sloan-Kettering) to embark on a seemingly simple experiment. The idea was to ask if we could use the classic micrococcal nuclease assay to define nucleosome positioning on a DNA template. But rather than using a short stretch of DNA that could be assessed by radioactive end-labeling and slab gel analysis, we decided the time was right to go “full-genome”. Accordingly, the template was all ~12.5mB of the yeast genome. Will systematically worked out conditions appropriate for hybridization, wrote the software to extract signal off the array (we were flying blind as the array did not come with an instruction manual) and producing an output that was compatible with the genome browsers of the time. Will’s computational background proved critical here (and at several later stages of the project). The result of this experiment was a map of the yeast genome with each of its approximately 70,000 nucleosome's charted with respect to their occupancy (the length of time that the nucleosomes spend in contact with the DNA) and positioning (the location of a particular nucleosome relative to specific sequence coordinates) in a logarithmically growing population of cells (the paper). Both occupancy and positioning regulate access of most trans-acting factors for all DNA transactions. Working with my new colleague Tim Hughes at the University of Toronto, we began to mine this data focusing first on how the diverse occupancy patterns correlated with aspects of transcription, e.g. the presence of transcription factor binding sites, the level of expression of particular genes, and the like. With this data for the entire genome, we could systematically correlate nucleosome positioning/occupancy with functional elements, sequence logos and structural features. Des Tillo, a graduate student in Tim’s lab and now a research fellow with Eran Segal, was able to build a model that could predict nucleosome occupancy. The correlation (R=0.45) was not great but it was miles better than anything that existed at the time. Tim and Eran’s labs, work with Jason Lieb and Jonathan Widom, refined the model to greater accuracy 2009 model.

Our original study (essentially a control experiment to define the benchmark nucleosome map in yeast) has been widely cited- many of these cites have come from what were two opposing camps, the sequence advocates and the trans-acting proponents. The sequence folks posed that nucleosome position is directed by the underlying sequence information while the trans-acting folks see chromatin remodelers as having the primary role. Having last worked on chromatin in 1995 as a postdoc in Lorraine Pillus’ lab (cloning yeast SET1), it has been a scientific treat to be both a participant and observer in this most recent renaissance of chromatin glory.

The protocol

As a reminder, the micrococcal nuclease (MNase) assay relies on the preference of this nuclease to digest linker DNA. By chemically crosslinking histones to DNA with formaldehyde, digesting with MNase, then reversing the crosslinks and deproteinizing the DNA, you obtain 2 populations of DNAs, those protected by digestion (and presumably wrapped around nucleosomes in vivo) and a control sample that is crosslinked but not digested (genomic DNA). The former sample becomes the numerator and the latter the denominator and you take the ration between the two. Initially we compared the microarray signal intensities, now next generation sequence counts are used to define nucleosomal DNA. This cartoon depicts the array based assay, but simply swap in an NGS library step for the arrays to upgrade to the current state-of-the-art.  




In 2007 we were restricted to array-based assays (as were most genomic studies) and frankly, the 4bp resolution of the arrays was pretty amazing. But the introduction of Next-generation sequencing opened up the possibility of charting nucleosomes in worms or wildebeest or almonds, there was nothing to stop you other than the short read lengths at the time. The read length issue has since disappeared as the “short-read” platforms can easily cover the length of a nucleosome protected DNA fragment of ~150bases.

12.12.12 on 12.12.12

Sorry - just had to have a post at 12.12.12 on 12.12.12.

Tuesday, December 11, 2012

Award: Ridiculous, absurd, offensive overselling of the microbiome from Chalmers & Gothenburg

Wow.  This is painful.  There is a press release that came out a few days ago: Changes in the gut bacteria protect against stroke.  In it they report on a new paper showing some interesting results comparing the metagenomes of gut microbiota in stroke patients vs healthy patients.  They found some interesting differences.  And they then made absurd, dangerous, self-serving claims that completely confuse the issue of correlation vs. causation.

Basically, they found carotenoid production genes to be more abundant in the people who were healthy.  And they then appear to have concluded that production of carotenoids by bacteria in the gut protects from strokes.  Completely ridiculous.  No evidence whatsoever is presented that such production of carotenoids by gut microbes does anything of the kind.   Compare the semi careful wording in the paper
Our finding of enriched levels of phytoene dehydrogenase in the metagenomes of healthy controls and its association with elevated levels of β-carotene in the serum may indicate that the possible production of this anti-oxidant by the gut microbiota may have a positive health benefit
To the drivel in the release
Our results indicate that long-term exposure to carotenoids, through production by the bacteria in the digestive system, has important health benefits. These results should make it possible to develop new probiotics. We think that the bacterial species in the probiotics would establish themselves as a permanent culture in the gut and have a long-term effect

Guest post on "The phone microbiome" from Georgia Barguil in Jack Gilbert's lab

From @Artologica on Etsy.  The Phonome. 
Today we have a very special guest post from Georgia Barguil in Jack Gilbert's group at University of Chicago / Argonne National Lab.  Georgia has been coordinating analyses of microbial surveys that have been a collaboration between me and Jack (although really driven by Jack and his lab in most ways).  The study subject: cell phones and shoes.  The study locations: conferences and meetings in order to have participation in microbial surveys by "citizen" scientists of one kind or another.  We did this together at the AAAS meeting.  And then Gilbert's lab did this at ThirstDC.  And then I did this at SciFoo at Google HQ.  We are working on a paper on this and wanted to get some results out to the community so Georgia wrote up this post.


Ever wanted to know what bacteria are on your shoes and phones? Of course you have! Here we explored the bacteria that call shoes and phones home; the shoes and phones belonged to employees at Google’s Headquarters, and to participants at the Thirst DC and AAAS annual meeting conferences over 2012 (Fig. 1). Altogether, 84 phones (34 from GoogleHQ, 23 from ThirstDC and 27 from AAAS) and 68 shoes (15 from SciFoo, 24 from ThirstDC and 29 from AAAS) were sampled. The DNA of these samples was extracted and the bacteria were identified by sequencing and subsequent computational analysis of a key gene (16SrRNA) found in all bacteria. Here we show some of the results.

Fig. 1: Map showing the 3 sampling locations: AAAS in Vancouver, SciFoo in California and ThirstDC in Washington

There are quite a lot of microorganisms found in these environments, as you can see in the graph below (Fig. 2), where each bar represents a sample and each color represents a group of bacteria. Also by looking at the chart you can see that the bacteria that live on phones and shoes are different, and found in different proportions. Actually, by comparing the bacterial profile from an unidentified sample with this collection, we could tell you whether that sample was from a phone or a shoe!

Fig. 2: Genus-level diversity and abundance of bacteria associated to phone and shoe samples.

In the shoe samples you can see a lot more colors, which implies that the shoes are home to more bacterial groups than the phones. Out of 560 groups of bacteria found, there were 90 that favored either shoes or phones; 70 of these groups favored the shoe environment while the other 20 favored the phone. Some of the groups that preferred the phones were:

Some fun holiday reading about the UC Davis Medical Center neurosurgeon saga

Well, here are some new news stories to read:
For some background see my detailed post with much of the history in the story here.

I must say, it certainly seems time to replace the administration at the UC Davis Medical Center.  The Dean is stepping down, but not for some months (see Amid controversy, Claire Pomeroy to step down as UC Davis med).  The main administrator Ann Madden Rice is still there.  I wouldn't expect her to stay for long.

Saturday, December 08, 2012

Attention all metagenomicists: put your pinky in the corner of your mouth & say "1 million dollars"

Already posted this to Twitter and Facebook but had to post here too.  This is wild.  DTRA has announced a $1 million prize for metagenomic analysis: DTRA Algorithm Challenge | Landing Page.  From their page
The Prize:
As nth generation DNA sequencing technology moves out of the research lab and closer to the diagnostician's desktop, the process bottleneck will quickly become information processing. The Defense Threat Reduction Agency (DTRA) and the Department of Defense are interested in averting this logjam by fostering the development of new diagnostic algorithms capable of processing sequence data rapidly in a realistic, moderate-to-low resource setting. With this goal in mind, DTRA is sponsoring an algorithm development challenge. 
The Challenge:
Given raw sequence read data from a complex diagnostic sample, what algorithm can most rapidly and accurately characterize the sample, with the least computational overhead?

My instinct is to keep this to myself because, well, I want to win.  But my sharing side of things won out and I am posting here.  Maybe we (i..e, the community) can develop an open, collaborative project to do this?  Just a thought ...


Friday, December 07, 2012

Get the genomes of up to 12 type strains of bacteria and/or archaea sequenced, for free

Barny Whitman asked me to post this announcement and, well, I am.  I made one edit below (see strikethrough) in honor of Norm Pace.


Genomic Sequencing of Prokaryotic Bacterial and Archaeal Type Strains

The Community Sequencing Program (CSP) Quarterly Microbial call of the DOE Joint Genomes Institute provides a great opportunity to obtain draft genomic sequences of the type strains of bacterial and archaeal species. The type strains may also include proposed species prior to publication. Type strains must be relevant to DOE mission areas, such as bioenergy, biogeochemistry, bioremediation, carbon cycling, and phylogenetic diversity. However, strains of human pathogens and human associated species are not eligible. Proposals for genome sequencing of type strains can be submitted through the CSP Quarterly Microbial call, whose deadline is December 17, 2012, with approval usually being completed within one month. Up to 12 strains can be included in each proposal. Proposals for larger numbers of strains need to be submitted to the CSP annual call in the spring. If you cannot make the December call, Quarterly calls are also scheduled for March 25, June 17, and September 23, 2013.

Proposals may be completed on-line at: http://proposals.jgi-psf.org/proposals. You will need to register and sign in to this server. Once on the server, follow the links to the “CSP Quarterly Microbial/Metagenome”. All strains will have to have been deposited in a culture collection, including proposed type strains prior to publication. If a culture collection ID is not available, you can attach a copy of the Certification of Availability. Once approved, you will need to provide 5-10 µg of high molecular weight DNA.

For questions, contact Barny Whitman, University of Georgia (whitman@uga.edu).

Wednesday, December 05, 2012

Further signs that microbiome work is getting hot: more $$ from NIH

Just got an email about this NIH program: RFA-RM-12-021: Evaluation of Multi-omic Data in Understanding the Human Microbiomes Role in Health and Disease (U54)

Some key points
  • Up to 3$ million per year
  • 1 or 2 awards
  • U54 Specialized Center
The human microbiome is, well, hot, and there continues to be money available to work on it ...


Guest post: uBiome puts microbiome science in the hands of the people

It is a fascinating time to be doing microbiology. One of the latest occurrences is the spread of work on the human microbiome and even more recently the launching of several crowdfunding / citizen science efforts in this area. (Full disclosure - I am a collaborator on one of these efforts - the American Gut Project).  Another one of these efforts is a startup called uBiome. After seeing the announcement of their launch I asked Zac Apte, one of the founders, if he would be interested in writing a guest post for my blog on what they are doing. And, well, he agreed. And it is below (the post title "uBiome puts microbiome science in the hands of the people is from him too - I added the pic).



uBiome puts microbiome science in the hands of the people



Most people think “germs” is a dirty word. That’s what we’re taught since preschool. But the truth is that microbes aren’t just good or bad -- it’s a lot more complicated than that. We are surrounded by microbes (on and inside of us) that form a complex ecosystem that supports and nourishes our health.

uBiome (www.indiegogo.com/ubiome) is a citizen science startup focused on allowing people direct access to this cutting ed research. By amassing a large set of microbiome samples along with health and lifestyle data, we will perform a microbiome-wide association study, examining specific traits as well as diseases such as diabetes, heart disease, hypertension, and depression in the context of the human microbiome.

We hope participants will join our community and track themselves in the long term -- as you change your diet or exercise regime, begin taking a new medication, such as an antibiotic, or simply as you age. Now is a great time for a first data point.

Finally, we’re not just polling people for their poop. We’re also polling them for their creativity in scientific research. When our first dataset goes live, we’re going to ask our citizen scientists to form their own cohorts and we’ll empower them (statistically speaking) to test their own hypotheses. That’s our vision.

Our team has expertise in metagenomics as well as roots in population genetics, computer science, and network mathematics. We also have a team of scientific advisors which includes inventor and MacArthur Genius award winner Dr. Joseph DeRisi, biotechnology pioneer and inventor of the recombinant Hepatitis B vaccine Pablo Valenzuela, as well as doctors, bioinformaticians, and researchers.

We really appreciate Jonathan Eisen reaching out to give us this opportunity to say hello on the Tree of Life blog -- and we look forward to engaging with you!

By Zac, Will and Jessica - the uBiome team

Monday, December 03, 2012

People not Projects: the Moore Foundation continues to revolutionize marine microbiology w/ its Investigator program

People not Projects.

It is such a simple concept.  But it is so powerful.  I first became aware of this idea as it relates to funding scientific research in regard to the Howard Hughes Medical Institute's Investigator program.  Their approach (along with a decent chunk of money) has helped revolutionize biomedical science.  And thus I was personally thrilled to see the introduction of this concept in the area of Marine Microbiology a few years back with the Gordon and Betty Moore Foundation's "Marine Microbiology Initiative Investigator" program.  Launched in 2004 it helped revolutionize marine microbiology studies in the same way HHMI's investigator program revolutionized biomedical studies.


The first GBMF MMI Investigator program ran from 2004 -2012. And the people supported were pretty darn special:
Now I am I suppose a little biased in this because at the same time GBMF launched this program they also put a bunch of money into the general area of Marine Microbiology and I have been the recipient of some of that money.  For example, I got a small amount of money as part of the GBMF Funded work at the J. Craig Venter Institute on the Sargasso Sea and Global Ocean Sampling metagenomic sequencing projects and also had a subcontract from UCSD/JCVI to do some work as part of the "CAMERA" metagenomic database project.  I ended up being a coauthor on a diverse collection of papers associated with these projects including Sargasso metagenome and this review, and GOS1GOS2 and my stalking the 4th domain paper.

I am also a bit biased in that I have worked with many of the people on the initial MMI Investigator list some before, some after the awards including papers with Jen Martiny, Ed Delong, Alex Worden and Ginger Armbrust, and Mary Ann Moran.

But perhaps most relevant in terms of possible bias towards the Gordon and Betty Moore Foundation is that in 2007 my lab received funds through the MMI program for a collaborative project with Jessica Green and Katie Pollard for our "iSEEM" project on "Integrating Statistical, Ecological and Evolutionary analyses of Metagenomic Data" (see http://iseem.org) which was one of the most successful collaborations in which I have ever been involved.  This project produced something like a dozen papers and many major new developments in analyses of metagenomic data including 16S copy correction, sifting families, microbeDB, PD of metagenomes, WATERs, BioTorrents, AMPHORA. and STAP.  This project just ended but Katie Pollard and I just got additional funds from GBMF to continue related work.

So sure - I am biased.  But the program is simply great.  In the eight years since the initial grants the Gordon and Betty Moore Foundation has helped revolutionize marine microbiology.  And a lot of this came from the Investigator program and it's emphasis on people not projects.  I note - the Moore Foundation has clearly decided that this "people not projects" concept is a good one.  A few years ago they partnered with HHMI to launch a Plant Sciences Investigator Program  which I wrote about here.

It was thus with great excitement that I saw the call for applications for the second round of the MMI Investigator program.  I certainly pondered applying.  But for many reasons I decided not to.  And today the winners of this competition have been announced and, well, it is an very impressive crew:
Some of the same crowd as the previous round.  Some new people.  Some people not there from the previous round.  All of them are rock stars in their areas especially if one takes into account how senior they are (the more junior people are stars in development).  And all have done groundbreaking work in various areas relating to marine microbiology.  The organisms covered here run the gamut including viruses, bacteria, archaea, and microbial eukaryotes.  The areas of focus covered range from biogeochemistry to ecosystem modeling with everything in between.  It really is an impressive group. Delong pioneered metagenomics and helped launch studies of uncultured microbes in the oceans.  Karl has led the Hawaii Ocean Time series and done other brilliant work.  Sullivan and Rohwer and pushing the frontiers of viral studies in the oceans.  Allen, Armbrust, and Worden are among the leaders in genomic studies of microbial eukaryotes in the marine environment.   Dubilier, Bidle, Fuhrman and Follows Stocker (double listed Follows in original post ...) - though they focus on very different aspects of marine microbes - are helping lead the charge in understanding interactions across the domains of life in the marine environment.  Orphan, Saito, Deutsch, Follows and Pearson are on the cutting edge of biogeochemical studies and trying to link experimental studies of microbes to biogeochemistry of oceans.

The great thing about the "people not projects" concept is that the people funded here get to follow their own path.  They are not going to be constrained by the complications and sometime idiocy of the grant review process.  They in essence get to do whatever they want.  Freedom to follow their noses.  Or their guts.  Or whatever.  It is a refreshing concept and as mentioned above has been revolutionary in various areas of science.  There has been a slow but steady spread of the "people not projects" concept to various federal agencies too but it seems to be more of a private foundation type of strategy.  Federal Agencies are so risk averse in funding that this type of concept does not work well there.  I wish there was more.  But I am at least thankful for what HHMI and GBMF and Wellcome and Sloan and other private groups are doing in this regard.  Now - sure - all of these private foundations do not do everything perfectly.  They have blunders here and there like everyone else.  But without a doubt I think we need more of the People not Projects concept.

Oh - and another good thing.  GBMF is quite a big supporter of Open Science in it's various guises.  So one can expect much of the data, software, and papers from their funding to be widely and openly available.   

It is a grand time to be doing microbiology largely due to revolutions in technology and also to changes in the way we view microbes on the planet.  It is an even grander time to be doing marine microbiology due to the dedication of the Gordon and Betty Moore Foundation to this important topic.  

Sunday, December 02, 2012

Twisted tree of life award #14: @nytimes and Nathaniel Rich on Immortal Jellyfish


Well, this article by Nathaniel Rich in today's New York Times Magazine certainly has gotten people talking: Can a Jellyfish Unlock the Secret of Immortality? - .  Alas, from a scientific point of view there are numerous problems with it.  So many that Paul Raeburn at the Knight Science Journalism Tracker at MIT has published a major takedown: First we get proof of heaven; now the secret of immortality. 

Now, the science about immortality in the article is certainly bad.  But that is not what I am here to discuss.  I am here to discuss the parts of the article about evolution.  I suppose if I had read the article online instead of in print I might have been attuned already to potential evolution problems from the correction on the first page
This article has been revised to reflect the following correction:
Correction: November 29, 2012
An earlier version of this article misstated the title of Charles Darwin’s classic book on the subject of evolution. It is “On The Origin of Species,” not “On the Origin of the Species.”
Oops.  Not a good start.  The article has a lot of background about jellyfish and in particular on person who is studying them and claiming this one species is immortal (which it is not).  It is the higher vs. lower organism meme that drives me crazy in the article:
Today the outermost twigs and buds of the Tree of Life are occupied by mammals and birds, while at the base of the trunk lie the most primitive phyla — Porifera (sponges), Platyhelminthes (flatworms), Cnidaria (jellyfish).
And then 
The mystery of life is not concealed in the higher animals,” Kubota told me. “It is concealed in the root. And at the root of the Tree of Life is the jellyfish. 
Seriously?  The root of the tree of life is the jellyfish?  And higher vs. lower organisms?  What exactly is a higher organism?  Does this mean that jellyfish have not evolved since their branch separate from the trunk of the animal tree?  Oh - and - what about the rest of the Tree of Life - you know - outside of animals for example?  Aaargh.  

The higher vs. lower meme continues with this quote:
Hydrozoans, he suggests, may have made a devil’s bargain. In exchange for simplicity — no head or tail, no vision, eating out of its own anus — they gained immortality.
Really?  So there is a tradeoff between complexity and immortality?  So does this mean all simple organisms are more immortal?  And all complex ones are doomed?  Where does this notion even come from?

For helping perpetuate the higher vs. lower organism meme (which drives me batty) I am awarding the author and the editor and the NY Times my coveted "Twisted Tree of Life" award.



As an aside, the article is littered with painful other statements like
It is possible to imagine a distant future in which most other species of life are extinct but the ocean will consist overwhelmingly of immortal jellyfish, a great gelatin consciousness everlasting.
So - this jellyfish operates in the absence of an ecosystem?  Suppose individual organisms are "immortal" as claimed in the article.  What exactly will they eat when everything else is gone?

Plus there is a conspiracy part that is lame.
You might expect that biotech multinationals would vie to copyright its genome; that a vast coalition of research scientists would seek to determine the mechanisms by which its cells aged in reverse; that pharmaceutical firms would try to appropriate its lessons for the purposes of human medicine; that governments would broker international accords to govern the future use of rejuvenating technology. But none of this happened.
Really?  So all the scientists and companies of the world have ignored this amazing finding?  Maybe, just maybe you might think that is because this is BOGUS?

And then there is the bogus "small bodied organism" problem.
He cited this as an example of a phenomenon he calls the Small’s Rule: small-bodied organisms are poorly studied relative to larger-bodied organisms. There are significantly more crab experts, for instance, than hydroid experts.
What?  Is this even remotely serious?  So ignore Drosophila as a model for animals.  Or mice for that matter.  Ignore Arabidopsis as a model for plants.  Ignore yeast too.  And E. coli.  Uggh.  Completely inane. 

Saturday, December 01, 2012

Drexel Executive Leadership in Academic Technology and Engineering program fellowships

Just a quick post here.  I just got an email about the ICELA | International Center for Executive Leadership in Academics program in "Leadership Development for Senior Academic Women".

The full email I received about this program is below:


Dear Colleague

As a recent recipient of an NSF institutional- level grant and a leader in your field, I would like to alert you to our (NSF-supported) leadership development program for mid-career women faculty in science and engineering.

The Executive Leadership in Academic Technology and Engineering program (ELATE at Drexel(r)) is a program for the enhancement of the professional and leadership skills of women faculty in mid-career (associate or full professor) in science and engineering fields. It is designed for faculty who are in a developmental phase of their institutional leadership, or who are already holding such positions.

We are now accepting applications for its 2013-2014 class through our online application<https://www.icela.net/apply/>.

The ELATE at Drexel program launched in 2012, and is currently hosting its inaugural class of Fellows from some of the nation's leading universities in science and engineering. Over the past year, the program has been recognized with awards from the National Science Foundation, the Sloan Foundation, and the Henry Luce Foundation.  Our greatest honor has been to work with the accomplished Fellows and faculty in the program. More information about the current fellows and faculty is available at http://www.drexel.edu/engineering/programs/special_opp/ELATE/

ELATE advances knowledge and skills in strategic finance and management, personal and professional leadership effectiveness, and academic organizational dynamics. Upon graduation, each ELATE fellow becomes part of a community of leaders in higher education that provides continuing support for each member and her organization while serving as role models for the next generation of men and women scientists and engineers.

We would appreciate it if you could distribute this information to your colleagues, and encourage women in current or potential leadership roles to apply. Information provided in the attached brochure.

Applications are due by January 3, 2013.

Questions? Please contact us at ELATE@Drexel.edu or 215-991-8240.