Wednesday, August 31, 2011

Bad science press release of the week: UC Merced on Circadian clocks in bacteria

Well, mind you, I like UC Merced and I sympathize with press offices and scientists who want publicity. But boy, this press release really got on my nerves: Professor Discovers Mechanism Behind Bacteria’s Biological Clock | University of California, Merced

Among the things I do not like in it:

"cyanobacteria, which is believed to be the oldest organism on Earth"
cyanobacteria refers to an entire Phylum not an organism and they are not "old" though there may have been cyanobacteria like taxa a long time ago

"All life — from bacteria to plants to humans — have evolved on Earth to anticipate sunrise and sunset"
- umm - cave organisms? deep sea organisms?

"These findings help pave the way for researchers who are studying the circadian rhythms of higher organisms"
- I hate the term "higher organisms" - it is meaningless to me

"Example of the campus’ innovative research toward health-related problems"
- circadian rhythms are really cool - I even worked on them previously - but the studies in cyanobacteria are not really health related - they are basic science

The science in this work might be cool. But I have a hard time getting past this press releases.

Sunday, August 28, 2011

An ecosystem in my house? Yes indeed. And with microbes too. #BostonGlobe #microBEnet

Well I am very excited about this article in the Boston Globe today: Ecosystem, sweet ecosystem - The Boston Globe. By Courtney Humphries the article discusses the Sloan Foundation program in the "Indoor Environment" that is focusing on microbial ecology of the built environment. I am, well, really into this area of work and have a grant from the Sloan Foundation in their program to crete something called "microBEnet" which stands for "microbiology of the Built Environment network." And in case you were wondering, yes, the BE is supposed to be capitalized and the m in microbe is not. My work in microBEnet is focused on Science 2.0 activities to help boost interaction and communication and outreach relating to studies of microbiology of the built environment. Check out the microBEnet site for more detail on that project (more on this in a bit).

Anyway, a little while ago I was interviewed by Courtney Humphries about studies of microbes in the built environment and the conversation seemed to go pretty well. And I kind of forgot about it due to some family things going on in my life. And then yesterday I saw the article. It is quite nice. It starts off with a nice drawing of a house making it look like an ecosystem

and the headline/lead in is really quite perfect "Ecosystem, sweet ecosystem." is the headline with the subtitle "What if we studies the indoors as an environment all it's own".  She goes on to quite Hal Levin (my collaborator on microBEnet), Jessica Green (the head of the BioBE center in Oregon focusing on biology of the built environment), me, Paula Olsiewski (the Program Officer at Sloan in charge of the Indoor Environment program) and Bill Nazaroff from Berkeley, who is also funded by the Sloan Foundation to work in this area.

The article is definitely worth a read.  Only issue really is that I have a feeling people may be distracted by some sort of storm hitting the East Coast right now.  Well, after the storm hits, microbiology of the indoor environment will likely be even more important to pay attention to.

If you want to brush up on studies of microbiology of the built environment check out some of the resources we have made and/or collated at microBEnet including:

Stay tuned for more, from microBEnet, from Sloan funded researchers, and from others studying microbiology of the built environment.  We spend on the order of 90% of our lives in built environments like buildings, cars, trains, etc.  It's about time we started studying such environments as ecosystems ...

Thursday, August 25, 2011

Twisted tree of life award #11: National Geographic for emphasizing Five Kingdoms & no Bacteria/Archaea

Well, I really don't want to complain so much but I guess I am on a roll recently.  And an email from Will Trimble pointed me to a news story that I cannot resist dissing a little bit.  The story is from National Geographic (86 Percent of Earth's Species Still Unknown?) and discusses the recent paper on number of species on Earth that I critiqued a bit in my last blog post: Bacteria & archaea don't get no respect from interesting but flawed #PLoSBio paper on # of species on the planet

The National Geographic article alas does not discuss the problems with the paper in terms of microbes (though Carl Zimmer's NY Times article How Many Species on Earth? It’s Tricky does as does a Google Plus post from Ed Yong. But that is not what I am here to moan about.  I am here to give out an award - a Twisted Tree of Life Award.  You see, I give this out when people who should generally know better do something bad relating to evolution.  And National Geographic (or, well, Traci Watson, the author) did in this article.  The complaint I have is the emphasis on the Five Kingdoms.  She writes.
Scientists lump similar species together into a broader grouping called a genus, similar genera into a still broader category called a family, and so on, all the way up to a supercategory called a kingdom..... There are five kingdoms: animals, plants, fungi, chromists—including one-celled plants such as diatoms—and protozoa, or one-celled organisms.

Tuesday, August 23, 2011

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:

Friday, August 19, 2011

I'd like some open science please

Check out some of the videos from last year's Open Science Summit. I like the first one below, especially since I am wearing my SciFoo shirt. I wore it because many of the people had to leave the Open Science meeting early to go to SciFoo and I was not invited ... do you hear that SciFoo organizers?

Get to know Jack & the story behind the paper by @gilbertjacka "Defining seasonal marine microbial community dynamics" A few days ago I became aware of the publication of a cool new paper: "Defining seasonal marine microbial community dynamics" by Jack A. Gilbert, Joshua A Steele, J Gregory Caporaso, Lars Steinbr├╝ck, Jens Reeder, Ben Temperton, Susan Huse, Alice C McHardy, Rob Knight, Ian Joint, Paul Somerfield, Jed A Fuhrman and Dawn Field.  The paper was published in the ISME Journal and is freely available using the ISME Open option. If you want to know more about Jack (in case you don't know Jack, or don't know jack about Jack) check out some of his rantings material on the web like his Google Scholar page, and his twitter feed, his LinkedIn page, his U. Chicago page. But rather than tell you about Jack or the paper, I thought I would send some questions to the first author, Jack Gilbert and see if I could get some of the "story behind the paper" out of him.  Since Jack likes to talk (and email and do things on the web), I figured it was highly likely I could get some good answers.  And indeed I was right. Here are his answers to my quickly written up questions (been out of the office due to family illness)

Thursday, August 18, 2011

Wow - back to the past with the AMCAS medical school application letter writing system

Well, this is enlightening in many ways.  Today I went to upload a letter of recommendation for someone in my lab for medical school.  I was instructed to go to the AMCAS web site and register and then submit the letter.   AMCAS is the "American Medical College Application Service".  I have never used it before.

So I went to the site to register. And I got an error message

Unsupported Browser
Please click here to view a list of browsers currently supported by AMCAS.
Need help? Contact us at

Some recent posts (of mine) from on microbes of the built environment that may be of interest

Just thought I would post a little list here of some recent blog posts I have made at a relatively new blog for my microBEnet project.  I may cross post occasionally but for now just going to post a list:
Would love it if people checked out the blog: and the web site and let me know what you think.   

Open Parkinson's - Parkinson's UK pushing (and funding) openness #brilliant

Just a quick post here on my new theme of Openness in Parkinson's research in honor of my father in law Carlos Benito who is, unfortunately, dying from this disease.  I did a google search for open access and Parkinson's to see whether any organizations out there were pushing for more openness.  And the good news is that there are a few.  One I highlight today Parkinson's UK.  I highlight them because of their position on Open Access publishing: Parkinson's UK - Open access publishing - (formerly Parkinson's Disease Society)

From their site:
"We expect authors of research papers to maximise the opportunities to make their results available for free."
But that is not all - they do offer to help support OA publishing fees on top of the research money they dole out.  Truly putting one's money where one's mouth is.

Wednesday, August 17, 2011

Single annual cycle for the National Science Foundation's MCB, DEB and IOS Divisions.

Just received this from NSF and thought it might be of interest to some:

Dear Colleagues:

The Directorate for Biological Sciences (BIO) of the National Science Foundation (NSF) has initiated new procedures for the submission and review of regular research proposals to the core programs within the Division of Molecular and Cellular Biosciences (MCB), Division of Environmental Biology (DEB), and Division of Integrative Organismal Systems (IOS). The changes for MCB were previously announced in a new solicitation (NSF-11-545).

Effective immediately, DEB and IOS will both operate on a single annual cycle of preliminary and full proposals. The initial deadlines for preliminary proposals will be in January, 2012 and the initial deadline for invited full proposals will be in August, 2012. New Solicitations NSF 11-573 (for DEB) and NSF 11-572 (for IOS) provide further details. Also see the Dear Colleague Letter NSF 11-078 and Frequently Asked Questions NSF 11-079 for additional information.

Both DEB and IOS will be hosting webinars to provide further information, please see the Division websites, (DEB) and (IOS), for details and contact information if you have questions or concerns. 

Tuesday, August 16, 2011

More fun with Mendeley plug ins for reference management #thingsIshouldhaveknownabout

OK - so I am a bit slow. I have been using Mendeley a lot recently. It has all sorts of nice "Social Networking" features for sharing reference lists and publications. I have for example used it as part of my push to free up papers by my father: Freeing my father's publications part 5: near completion of PDF collection at Mendeley (h/t @David_Dobbs). And I have created some groups on Mendeley for sharing publications relating to various topics in which I am interested including: Microbial Forensics, Microbiology of the Built Environment and Phylogenetic and related analyses of metagenomic data. I have experimented with other online reference management systems like CiteULike, Connotea, Zotero, etc and each have some nice features. I have even written up some more detail on how to use citeulike for one project: Introducing citeulike group on microbiology of the built environment ....

 But it is the more elaborate social networking features that drew me to Mendeley and why I am using it more than the other online system.  And I have focused for example on getting all my personal publication in there to share them with others. And I confess I did not pay attention to many of the other features.

Yesterday however I discovered that Mendeley has plug-ins for generating bibliographies in various word processing programs: Reference Manager | Mendeley. Obviously I probably should have known this. But I have been using EndNote forever and had not experimented with anything new in a while. But I tried out the Mendeley Plugin for MS Word and it is OK. Not perfect. Still needs some work. But it is another factor in why I will likely shift even more to using Mendeley over other system. Still will play with the other ones out there ... so if people have comments or suggestions please post.

Plus see below for an example of some of the Mendeley embed widgets one can make

What is in a name? A case study of genomic epidemiology w/ Bacillus cereus and Bacillus anthracis There is a very interesting new paper that just came online in the Archives of Pathology: Rapidly Progressive, Fatal, Inhalation Anthrax-Like Infection in a Human: Case Report, Pathogen Genome Sequencing, Pathology, and Coordinated Response

I was alerted to the paper by Eileen Choffnes of the National Academy of Sciences Institute of Medicine Forum on Microbial Threats (which I am a member of).  In the paper, James Musser, Angela Wright and colleagues, the authors discuss the use of genome sequencing in the characterization of a fatal infection with a bacterium that appeared to be a species of Bacillus.  Their summary is below and pretty much sums it up:

Saturday, August 13, 2011

Finally updated my blog template after, oh, five years

Well, after breaking the html behind my blog template many times with all sorts of hacked code for widgets and trackers and other things.  I have decided to clean up my act.  And just revert to a standardized Blogger template for now.  If some things are missing, maybe I will revert.  The colors I am going to play with - not sure if I want something new or to go back to the old ones.  But for now, there will be a bit of a new look here.

Friday, August 12, 2011

Open Parkinson's - need for more progress on Open Access for papers on Parkinson's

I have a new aspect of open science I am concerned about. It is research on Parkinson's. This comes from having a family member with Parkinson's who is not doing so well. And I am getting frustrated with trying to read up on some Parkinson's related research but hitting a paywall for much of it. Uggh. This is so incredibly annoying and, in many ways, immoral. If we want to speed up the work towards cures, treatments and prevention strategies, we need to share more broadly everything we know about this disease. Yes, I know - publishing costs money. And yes, I know, open access and open science does not in any way solve all the problems associated with scientific and medical discovery and research. But I do know that openness can accelerate the pace of progress.

If you look at "openness" in relation to Parkinson's studies it is pretty disappointing. For example, of 60,400 publications that come up in Pubmed with a simple search for "Parkinson's" 9053 have free full text available. That's is just not enough. One thing that is interesting (and disconcerting) is what it looks like over time:

Fun with marketing #numerology

Just got an email marketing a new book on numerology.  I have a feeling, just a slight one, the marketer does not know much about me. But I thought I would share so everyone can ponder numerology. In order to spare people if they are not interested I have put everything below the "jump break"

Wednesday, August 10, 2011

Hydrogen as a fuel? No this is not about cars, this is about animals and their symbionts in the deep sea As many of you know, I generally avoid writing about non open access publications here.  But occasionally I make exceptions.  And I am making one today.  There is a wicked cool paper out in Nature today.  Entitled "Hydrogen is an energy source for hydrothermal vent symbioses" comes from Nicole Dubilier, Jillian Petersen and others.  It is about my favorite ecosystem(s) on the planet - hydrothermal vents.  I became interested in these vents in 1989 when I met Colleen Cavanaugh who at the time was a Junior Fellow at Harvard.  She told me about her work on bacteria that live inside tubeworms, clams and other creatures in the deep sea that are key to the lives of these animals.  The bacteria are chemosynthetic (i.e., they use the energy of chemicals to drive carbon fixation).  The animals have either no digestive systems or very degenerate ones and the bacteria function much like chloroplasts do for plants.  The bacteria basically make everything for their hosts while the hosts collect energy (chemicals in this case) and oxygen and CO2 for the microbes.

After hearing Colleen tell me about her work on these symbioses and how at the time nobody knew much about the symbionts, I joined her new lab at Harvard (she was just appointed as a junior professor) and worked in her lab in my Senior year and after graduating (and ended up publishing my first paper on symbionts of a clam Solemya velum).  I have been captivated by symbioses ever since.  So much so that many years later I worked with Colleen, Irene Netwon, Tanya Woyke, Dongying Wu and others to sequence and analyze the first genome of any of the chemosynthetic symbiotic bacteria.

Organic farming and antibiotic resistant bacteria:

Well, this news story is certainly going to get some publicity and almost certainly some responses. The Washington Post and Baltimore Sun are reporting on a new paper: Lower Prevalence of Antibiotic-resistant Enterococci On U.S. Conventional Poultry Farms That Transitioned to Organic Practices. The paper is from Environmental Health Perspectives - an open access journal so anyone out there can check it out. However, you might want to start with the news stories:

Organic farming reduces resistance of bacteria to antibiotics, study finds - The Checkup - The Washington Post

In summary - the researchers cultured microbes from poultry farms - including conventional ones as well as ones that recently switched from conventional to organic practices. And though potentially unpleasant types of microbes were found everywhere, the percentage of those microbes that were resistant to antibiotics was much higher at the conventional farms than the newly organic ones. Not surprising to me or to many others. But at least someone is studying it. In general (from other word), it seems like we desperately need to reduce antibiotic usage on farms --- to limit the potential selection for and spread of antibiotic resistance. But general recommendations are less useful than specific studies. Hopefully this study is sound and will get a lot of press.

Monday, August 08, 2011

Uggh: "Barcoding" researchers keep ignoring microbes and history #antimicrobiites #annoying

Barcoding is a technique in which researchers sequence a small region of the genome of an organism and use this sequence information as a "tag" to identify species/types.   The term barcoding is most commonly associated with sequencing a small portion of the mitochondrial genome of a multicellular eukaryote.  There is a new paper in PLoS One discussing barcoding: Neotropical Bats: Estimating Species Diversity with DNA Barcodes.  The paper seems potentially interesting.  But I could not get past the part where they write "To the best of our knowledge, it is one of the largest molecular surveys of biodiversity."

Let's examine this statement a bit.  In the study here the authors did a heroic task - they did barcoding for some 9000 individuals.  It is impressive, in many ways.  But one can only call it a large molecular survey of biodiversity if one thinks  biodiversity = plants and animals. If however you include microbes, as of course you should, then this new study is not even remotely the "largest molecular survey of biodiversity."  In fact, one could argue that 100s if not 1000s of studies of biodiversity of microbes are "larger" in many ways than this study.  In microbial studies 9000 "individuals" are characterized routinely in most studies via the use of collecting DNA from environmental samples and sequencing genes from 100s -1000s to even billions of individual cells in a sample.  This is done routinely in both metagenomic work (where one collects DNA from the environment and randomly sequences it) or ribosomal RNA PCR surveys where one collects DNA and then sequences rRNA genes from the sample.  Overall, hundreds of microbial studies cover more biodiversity than this one - more species - wider phylogenetic diversity - more samples even.

Saturday, August 06, 2011

New paper from my lab (& the Facciotti lab): Mauve Assembly Metrics #Halophiles #Genomics

Just a quick post here. A new paper from my lab has come out in Bioinformatics. The paper is relatively simple. Titled "Mauve Assembly Metrics" it reports work of Aaron Darling and Andrew Tritt (with some minor contributions from me and Marc Facciotti). Aaron wrote the program Mauve when he was a student in Nicole Perna's lab at Wisconsin: Mauve: multiple alignment of conserved genomic sequence with rearrangements. Over the years he (and others) have continued to develop the program and written a few papers too including for example, the development of progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. This new paper reports basically a system/scripts to measure assembly quality. Here is the abstract:
High throughput DNA sequencing technologies have spurred the development of numerous novel methods for genome assembly. With few exceptions, these algorithms are heuristic and require one or more parameters to be manually set by the user. One approach to parameter tuning involves assembling data from an organism with an available high quality reference genome, and measuring assembly accuracy using some metrics. We developed a system to measure assembly quality under several scoring metrics, and to compare assembly quality across a variety of assemblers, sequence data types, and parameter choices. When used in conjunction with training data such as a high quality reference genome and sequence reads from the same organism, our program can be used to manually identify an optimal sequencing and assembly strategy for de novo sequencing of related organisms.

Check out the paper: Mauve Assembly Metrics. Download the scripts/code and Mauve and play around and let me know what you think.

Note this paper was supported by a grant from the National Science Foundation (ER 0949453). That grant is focused on comparative genomics (sequencing and analysis) of halophlic archaea. Stay tuned for more on that project as we are writing up a series of papers ....

Some related links:

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