Wednesday, December 22, 2010

Taking a much needed blogging/twitter/etc break for a few weeks

Well, am on Winter Break here at Davis and am going to be taking at least a few weeks off of blogging/twitter/etc.  And trying to ignore email too.  I know - probably some irony in posting about taking a break, but whatever ... am really taking a break.

Best wishes to all out there and see you next year ....

Tuesday, December 07, 2010

NASA arsenic story - let's lay off the personal attacks on all sides

I have many thoughts about the recent NASA - arsenic - microbe story.

Quick summary
  1. NASA announced a major press conference
  2. at the conference they discussed a new Science paper claiming to show the discovery of a microbe that could replace much/some of its phosphate with arsenic
  3. initial press coverage of the paper was very positive and discussed the work as having profound implications for understanding of life in the universe - though some scientists in some of the stories expressed skepticism of the findings
  4. subsequently many science bloggers further critiqued the paper and/or the press coverage
  5. NASA and the scientists have now refused to discuss the criticisms of their work and press interactions
  6. News stories have now come out summarizing the blogger criticisms and also discussing the unwillingness of NASA / the authors to discuss their work
As I said above I have some strong opinions about the published paper and about the actions of many of the people involved.  For example I think NASA handled this whole thing very poorly.  And I think the unwillingness of the authors and NASA to discuss the work by saying such discussion should be done only in the "peer reviewed literature" is really unwise.  

But that is not what I am here to write about today.  I am here to beg for people to calm down on the personal criticisms and attacks of any of the players involved.  I have seen so much out there about the failings of the paper reviewers, about the intelligence of the authors and the bloggers critiquing the authors, and a whole lot of uneducated guesswork about why some of the things associated with this story happened the way they did.  I think it is perfectly fair to express opinions about the original paper, about the press releases and conferences and about the actions of any of the players here.  But I do not think it is reasonable to go beyond that and to attack the people themselves.  Let's try and make this an open discussion of science and science reporting and not a venue to spout derogatory comments about the people involved 




Monday, November 29, 2010

10 benefits (for my career) of blogging/tweeting/etc #fb

I was recently interviewed for a story in the Scientist by Bob Grant about blogging and related activities (see his story "You Aren't Blogging Yet here). As preparation for this interview I made a top 10 list of ways that blogging had been beneficial to me. And I thought I would post my list here. I note, I made this list in about 10 minutes so I am sure there are other things I could add, but it was REALLY easy to make the list so I think w/o a doubt there have been many many benefits ....


10 ways blogging/microblogging has been beneficial to my career:
  • Collaboration. Many of my current projects have collaborators that have come about in part via interaction on blog/Twitter. 
  • Concentration. I concentrate more at meetings since I am either planning on writing something about it, or am actually live blogging the meeting. 
  • Personnel. Some of the recent recruits to my lab have come about via connections online. 
  • Crowdsourcing. Asking questions on twitter and my blog has been a great way to rapidly find out information about a particular area. 
  • Reduced travel. I have two little kids and do not like to travel much right now for this and other reasons. Blogging and Twitter and other social networking activities help peole find out about my work without me having to travel. 
  • Outreach. Blogging and related activities are a good way to interact with public and scientists in other fields. 
  • Keeping up with cutting edge (mostly via twitter). Following the right people is a great way of finding out about the latest in various fields 
  • Great practice for explaining/teaching. In my head, I could explain anything. But when I actually try to explain in writing, I realize how many assumptions we make and how much jargon there is. Trying to explain to a broad audience is great practice. 
  • Record of my thoughts/ideas. I forget a lot of things. I am sure others do too. But twitter and my blog provide a good record of some thoughts I had on various topics. 
  • New $$. I have recent gotten a new grant mostly due to my activities in the Science 2.0 world and I think my activities like blogging, etc also could in principle help get other grants where "outreach" is important. 
Anyway - just a little post about ways that blogging and tweeting have been helpful for my career. Other examples/areas that blogging and tweeting have helped people's careers in science would be welcome here ...

Friday, November 26, 2010

Quick post - congrats to Jill Banfield, environmental #microbiology guru, for winning Franklin Medal & L'Oreal-UNESCO award

Very cool news from UC Berkeley.  Jill Banfield, one of the greats of environmental microbiology, is going to receive both the Benjamin Franklin Medal in Earth and Environmental Science and the L'Oreal-UNESCO "for women in science" award.

I am very happy to see this.  Jill has done some amazing work in multiple areas of environmental microbiology and continues to push frontiers in technology and science.  And since I am always on an Open Access crusade here, here are some links to some of her recent papers that are free in Pubmed Central:

Tuesday, November 23, 2010

A very simple suggestion for scientists to increase their interactions w/ people in the humanities

Well, I have been inspired recently by some of my interactions with people in the humanities. In general I think that there need to be more professional interactions between scientists and people in the humanities. So here is a simple suggestion, that could be taken up by scientists.

When you go to give a talk at another place, and your hosts ask who you want to meet with, include someone from outside the sciences. Either find someone yourself or asks your hosts to do it. I am going to do this for all my future visits to other campuses. Not only might it help in terms of interactions across fields, but I know my brain hurts after a full day of meeting with only scientists, so this has got to be better ...

Monday, November 15, 2010

Another good paper, but bad omics word of the day: uniqueome

Wow. This is bad. Really not much to say here other than to point you to a new paper by Koehler et al in Bioinformatics:

The Uniqueome: A mappability resource for short-tag sequencing — Bioinformatics

Paper seems useful. The word. It is simply awful. And the winner of today's "Bad omics word of the day".  Hat tips to @leomrtns and @neilfws 


From "The Uniqueome: A mappability resource for short-tag sequencing
Ryan Koehler, Hadar Issac , Nicole Cloonan,*, and Sean M. Grimmond." Bioinformatics (2010) doi: 10.1093/bioinformatics 







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

Sunday, November 14, 2010

Good paper but bad omics word of the day: drugome

Already tweeted about this but felt it had to be given more prominent status. There is a new, interesting paper in PLoS Computation Biology: The Mycobacterium tuberculosis Drugome and Its Polypharmacological Implications

But that word - drugome. Here is their definition
The resulting drug-target interaction network for all structurally characterized approved drugs bound to putative M.tb receptors, we refer to as the ‘TB-drugome’
I really do not think they need to make that into a "ome" word. Mind you, the study is cool and useful. But that word. It is not very good. And thus they are winners of my "Bad omics word of the day" award.


Figure 2. A protein-drug interaction network to illustrate similarities between the binding sites of M.tb proteins (blue), and binding sites containing approved drugs (red). From Kinnings SL, Xie L, Fung KH, Jackson RM, Xie L, et al. (2010) The Mycobacterium tuberculosis Drugome and Its Polypharmacological Implications. PLoS Comput Biol 6(11): e1000976. doi:10.1371/journal.pcbi.1000976 




Hat tip to @7T1 and @dgaston83 and @toranaga for pointing this one out.

Saturday, November 13, 2010

YARFOA: Yet another reason for #OpenAccess: speeding innovation in aquaculture

Just saw this interesting paper arguing that open access to literature is critical for the field of aquaculture. The paper argues that open access to literature has accelerate innovation by promoting more partnerships with hobbyists and with others who might normally be outside the "inner circle." Definitely worth a read and it fits under my "YARFOA" category - Yet Another Reason For Open Access.

The paper is "The importance of open access in technology transfer for marine ornamental aquaculture: The case of hobbyist-led breeding initiatives" from the Journal Aquaculture, Aquarium, Conservation & Legislation International Journal of the Bioflux Society.

It is is by Andrew Rhyne who is connected with the New England Aquarium and also at Roger Williams University.

I love the concluding paragraph by the way:

Opening the door to an open process. I would hope that others would join me in supporting the free flow of information by publishing their work in open access journals, and encouraging societies like the World Aquaculture Society, the American Fisheries Society, and European Aquaculture Society to go to an open access format. We should fully applaud blogging or posting on discussion forums in real time about efforts to rear new species or develop new live feeds. The dialog that occurs on MOFIB and other online forums can spark innovation that is not possible through traditional formats. I believe that open access is the key to faster breakthroughs, and to better translation between academia, hobbyists, and commercial industry. The Aquaculture field has an opportunity to become an exemplary model for all applied science fields: let’s seize it.

Friday, November 05, 2010

Good omics word of the day: transcriptomics

As many of you know, I spend a lot of time bashing #badomics words.  Some have asked if I just hate all omics words.  And the answer is no.  First, I am only annoyed by words that use "omics" or "ome" in the sense of "genomics" or "genome".  Thus words that use the "ome" suffix in the sense of a cellular complex (e.g., ribosome, proteosome, etc) are not on my radar.  And words that use "omics" in the sense of "economics" (e.g., Obamanomics") are not my concern either.  My problem is those that in essence are latching onto "genomics" excessively.

And on twitter as well as in my blog I have bashed many such #badomics words including vaccinomics, waveomics, adversomics, bibliome, epitheliome, nutriome, transactome, N-terminome, miRNAome, modomics, tRNomics, variome, Speechome, connectome, negatome, material degradomics, and many more.  I even give out two types of awards here in this regard: Worst New Omics Word Award and bad omics word of the day.  And alas, I am sure I will give out more.

But today I thought it might be useful to be positive.  And thus I am going to discuss what I view as a good omics word.  Not great mind you.  But pretty good.  And this is "transcriptomics" and its relative "transcriptome".  Both of these are pretty good words.

From Wikipedia here is the definition of transcriptome
The transcriptome is the set of all RNA molecules, including mRNA, rRNA, tRNA, and other non-coding RNA produced in one or a population of cells. The term can be applied to the total set of transcripts in a given organism, or to the specific subset of transcripts present in a particular cell type. 
This seems to be a perfectly reasonable and useful use of the "ome" suffix.  It is genomic in scale (i.e., all RNA in the cell - not like many badomics words which are too specific).  And it is broad in that it can be used to refer to all the RNA in an organism or cell or such.  The first use I have found is from this paper on yeast in 1997.    But there may be earlier examples.

Anyway - trying to be positive today.  And transcriptome to me is a good omics word.  

Thursday, October 28, 2010

The Story behind the Meeting: Lake Arrowhead Microbial Genomes 2010 #LAMG10

Well, I really wanted to write up some thoughtful piece about the Lake Arrowhead Microbial Genomes Meeting I just got back from.  But I am in the throes of prepping for beginning teaching a 700+ person class here at UC Davis and well, I just can't put enough effort into the meeting write up as I would like.  So perhaps my live blog page may be all that I will post directly about the meeting (and at the bottom of this post I am re-posting my feed from Friendfeed).

And if you want to see my slides here they are

And here is a little write up of sorts - more about the history of the meeting than this 2010 meeting.....

First, some background.  The Lake Arrowhead Microbial Genomes meeting was, well, in Lake Arrowhead California.  This is both a town and a lake and is in the San Bernadino Mountains East of Los Angeles.

Fortunately for all of us who were there, UCLA has a conference center in Lake Arrowhead, just off the lake itself.  And for the last at least 12 years, every two years, there is a meeting in September at this Conference Center that focuses on microbial genomes in one way or another.  The meeting has changed names, and has gone through a few different major financial supporters, but has always been organized in a large part by Jeffrey H. Miller from UCLA.  Do not confuse him, please, with Jeffrey F. Miller, another microbiologist from UCLA.  That would be a bad thing.  Sort of like confusing me with my brother Michael.

Anyway, Jeffrey H. Miller has been the major force behind organizing this meeting and he has always done a bang up job on fostering a great atmosphere for both science and interaction.  I am not sure what it is he does, but it always seems to work.  One component is that Miller clearly believe that a conference is not only about hearing talks.  Too many times recently I have been to meetings that were overscheduled with speakers and no time for relaxation or discussion or other activities (the Open Science Summit in Berkeley comes to mind - at that meeting I had to actually stage a coup of sorts to prevent the organizers from skipping lunch and all breaks just to have more talks).  At the Arrowhead meetings, Miller always leaves a few hours in the afternoons free and then has poster viewing/reception time before dinner, plus reception time after evening talks.  It works out well.

The Lake Arrowhead Microbial Genomes meeting has a bit of an unusual history.  It is in essence part of a yearly meeting that used to be go by the name "Small genomes." And every two years, it happens in Lake Arrowhead under the direction of Jeffrey H. Miller.  And since 1998 I have gone to this meeting each time it has come around: 1998, 2000, 2002, 2004, 2006, 2008, and now 2010.

It all started for me in 1998.  I originally signed up for the meeting to give a joint talk with A. John Clark.  I was finishing up my PhD at Stanford on Evolution of DNA Repair Genes, Proteins and Processes and had a post doc lined up to work with Clark at Berkeley.  John was the person who had discovered the recA gene many years before with his graduate student Ann Murgulies. Clark, Steven Sandler and others had been working on functional studies of archaeal homologs of recA and has recently turned their attention in collaboration with Norm Pace (who was then at Berkeley) to trying to use PCR amplification of the archaeal recA homologs to study uncultured archaea, much like Pace and others had done with rRNA. This was seemingly perfect for me as I had worked on both rRNA PCR of uncultured microbes and on evolution of recA (e.g., see here, here, and here) and on DNA repair in archaea.

Anyway, John was invited to give a talk at the Lake Arrowhead meeting and he asked if I would do a tag team talk with him where I could present the results of my phylogenomic analysis of DNA repair genes across the available genome sequences.  So I said sure.  I had no idea what I was getting into, but I went to the meeting.

Alas, there was some awkwardness there because after accepting the post-doc at Berkeley with Clark, I told him I was going to have to drop it.  That was because in the meantime I had finagled my way into going to a dinner with Craig Venter when he came to Stanford to give a talk.  At the dinner I proceeded to tell Craig that I thought some of the evolution stuff he was doing was sketchy and that the genome annotation at TIGR could be improved by phylogenetic analysis.  I drew on napkins, told him about some of my recent papers and eventually he invited me to interview for a job.  The interview went well and both I and my then fiancé now wife were both offered faculty jobs at Craig's institute "TIGR", which we accepted.

So here I was giving a joint talk with Clark yet had just told him I was ditching him for another job.  Well, we soldiered through - but the rest of the meeting went well.  I met all sorts of interesting people, developed multiple collaborations, and had a very good time.  Shortly thereafter I moved to TIGR and began life as a genome sequencer.  For more on the 1998 meeting, alas, there is not much out there on the web.  But I did find my meeting book and some notes and I scanned them in (see below).

Tuesday, October 12, 2010

Figuring out figures in scientific papers: new search / ranking method outline in PLoS One paper

Just a quick post here.  A colleague just sent me a link to her fascinating new paper in PLoS One: PLoS ONE: Automatic Figure Ranking and User Interfacing for Intelligent Figure Search

In this paper Hong Yu from the University of Wisconsin in Milwaukee describes a system for better automated characterization of figures from scientific papers.  The system is available through their webserver "Ask Hermes".

If you want to learn more about the system I suggest you read the paper.  Or watch their video.



Basically the general idea is summarized in their background section of the abstract:
Figures are important experimental results that are typically reported in full-text bioscience articles. Bioscience researchers need to access figures to validate research facts and to formulate or to test novel research hypotheses. On the other hand, the sheer volume of bioscience literature has made it difficult to access figures. Therefore, we are developing an intelligent figure search engine (http://figuresearch.askhermes.org). Existing research in figure search treats each figure equally, but we introduce a novel concept of “figure ranking”: figures appearing in a full-text biomedical article can be ranked by their contribution to the knowledge discovery.
I particularly like that they also allow searching just for open access figures, which may be of significant value to people who want to do things like make a slide presentation with no copyrighted/protected material in it.  For example see the results of a search for open access figures using the keyword phylogenomics.

Anyway - definitely worth checking this out.

Yu, H., Liu, F., & Ramesh, B. (2010). Automatic Figure Ranking and User Interfacing for Intelligent Figure Search PLoS ONE, 5 (10) DOI: 10.1371/journal.pone.0012983

Twisted Tree of Life Award #9: Nature News on the "Marsupial" platypus

OK, though this is not as bad as printing the wrong form of DNA on the cover Nature has another faux pas. In a recent Nature News story discussing a recent paper on the characterization of venoms in the platypus, Ewen Callaway reports in Poisonous platypuses confirm convergent evolution : Nature News:
By some accounts, being poisoned by a platypus could qualify as punishment in one of Dante's circles of hell. In one case report2, Australian doctors described their treatment of a 57-year-old man a few hours after he grabbed one of the small marsupials while fishing. The pain was "so bad I started to become incoherent" the man said, and far worse than the shrapnel wounds he took as a soldier. Ibuprofen and morphine provided no relief, and one finger was swollen and ached more than 4 months after the run-in.
The only problem with this is that the platypus is a monotreme, not a marsupial.

From http://kaboodle.nescent.org/?q=node/594
Fortunately Nature does get this correct on the headline for the story "Genome analysis shows that the monotremes and snakes have similar venoms" but the damage is done in the middle.

The mistake in the middle of the article may seem a very minor thing to most of you out there.  But @an_dre_a is calling for action on twitter from the monotreme antidefamation league.  And I am now posting here and giving Nature my coveted "Twisted Tree of Life Award" (the ninth) to bring attention to this horrendous horrendous offense to monotremes everywhere.

Hat tip to @recher_she on twitter who called my attention to the Nature article because it mentions the "venome" a really #badomics word that I will be writing about later. 

Sunday, October 10, 2010

10:10 AM on 10/10/10 Happy binary day

Just a quick happy binary day to all you 10101010101010101010101010101010 fans out there.

Saturday, October 09, 2010

Twisted Tree of Life Award #7 #8: Alroy on "Changing the rules of evolution"

Twisted Tree of Life
Every once in a while I give out an award here for bad discussions of evolution in the media or scientific publications. I call this the "Twisted Tree of Life Award." And here is a doozy. It comes from a recent paper in Science: The Shifting Balance of Diversity Among Major Marine Animal Groups -- Alroy 329 (5996): 1191 -- Science

The paper is actually pretty interesting. But the last line of the abstract. OMG. It is beyond awful. Here is the full abstract:
The fossil record demonstrates that each major taxonomic group has a consistent net rate of diversification and a limit to its species richness. It has been thought that long-term changes in the dominance of major taxonomic groups can be predicted from these characteristics. However, new analyses show that diversity limits may rise or fall in response to adaptive radiations or extinctions. These changes are idiosyncratic and occur at different times in each taxa. For example, the end-Permian mass extinction permanently reduced the diversity of important, previously dominant groups such as brachiopods and crinoids. The current global crisis may therefore permanently alter the biosphere’s taxonomic composition by changing the rules of evolution.
That last line saying that the current extinction crisis may change the rules of evolution really really really bugs me. Changing the rules? Please. If they are rules, then, just how, exactly do they change? If they do change, perhaps they should not be rules no?

And as an aside, what is up with Science not printing the full first name of authors? Does that really save space?

Anyway - not much to say here other than that J. Alroy is the winner of my the 8th "Twisted Tree of Life Award" for suggesting that the evidence presented in this Science paper changes the rules of evolution. And a half award goes to the editors of Science for letting this BS get into the abstract.

Previous recipients of this award are

Tuesday, October 05, 2010

Stanford Magazine and a veneer of science: helping the world buy "human pheromones"

Wow.  This ad for "Athena Pheromones" definitely caught my eye in Stanford Magazine in the September-October 2010 issue.   So I decided to scan it in and share.

The whole thing is, sadly, pretty lame actually.  These "pheromones" come from the Athena Institute, which they say was started by Winnifred Cutler who was a post doc at Stanford.  They claim, on their web site and in this ad, that she "Co-discovered human pheromones in 1986" and use this to I guess imply that whatever potions they sell must therefore work the way they claim.

Sure, the claims they make for what the potions they sell are not as outrageous as many things relating to sexual interactions.  In fact, they are pretty tame:

  • But 10X does this with the special power of human pheromones. 
  • Men who used 10X in their aftershave experienced increased romantic attention and affectionate behavior from women.
  • Some men report 10X improves their business relationships.
But what annoys me about this is the attempt to use science smoke and mirrors to support the claims.  As far as I can tell, they are using a series of tricks to make you think that this stuff really works.

First, they seem to be overinflating the scientific credentials of the founder of the company.  Sure she seems like she might be a decent scientist.  But they give her credit for the discovery of human pheromones.  And the evidence for this discovery is a bunch of news coverage from 1986.  But it seems from looking at the literature, not too many other scientists refer to these papers as having discovered human pheromones.  So my guess is one creatively written press release led to a lot of press and now, 24 years later they are still trying to ride the wave of publicity from the news coverage.

Second, they do some creative writing to make it seem that the scientific evidence of the effectiveness of the pheromones that they claim to include in their potions is overwhelming.  But upon closer examination, the work they cite is pretty minimal.  On one page they cite a poster abstract from a meeting in 1998.  On another they reference a 2002 paper by what appears to be an outside group that did a controlled trial of sorts - so at least there is some science here.  But it is pretty minimal.  Amazingly, and very annoyingly, if you want to read more detail about these studies they tell you: "to order reprint of full study click here)  and then you have to pay to get reprints.  

Third, and most troubling, is that it is very hard to figure out what exactly is in the little vials they sell for hundreds of dollars each.  Is it the same thing in the papers?  What is the concentration?  Is this homeopathic pheromonetherapy?  They say it is a trade secret - which does make some sense if it is real - but it is hard to evaluate without such information.

They must hope that we make the following connections (1) founder is a pioneer in scientific  studies of human pheromones (2) they have shown that some human pheromones really have effects (3) they sell vials supposedly with human pheromones -> therefore anyone interested in attracting more "mates" should buy the vials, since they must work. 

Many other aspects of the site are like this - referencing science, giving some sort of faux science veneer, but the science is actually pretty limited.  Not that I am saying human pheromones do not exist - most likely they do.  But is there something in these vials that is an effective human pheromone?  And if so, how much exactly do you get for $100?  My guess is, the true answers to these questions would lead most to stop buying this stuff.  

Sunday, October 03, 2010

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:

Saturday, October 02, 2010

Foundation: Nobel Prizes to be awarded via reality shows incl. Nobel Survivor, Sweden's Next Model (System) & The Amazing Particle Race

In a surprise last minute press release the Nobel Foundation has announced that this year's Nobel Prizes will be given out via reality show style competitions rather than by the traditional committee deliberations.

Marcus Snorch, Chairman of the Board of Directors of the Nobel Foundation said in at a press conference announcing the new system "We have noticed that in the last 5-10 years there has been a diminishing interest in the Nobel Prizes. This decrease appears linked to the steady increase in popularity of so-called reality show competitions. We felt like it was time for the Nobel Prize to try and attract a younger audience. Our reality Nobel series should be highly popular."

Barbara Connon, chairman of the Nobel Foundation Board of Trustees concurred, "We all felt like a shake up was necessary. The Nobel Prize is so important for the world, yet nobody was paying attention anymore. Our new approach, where semifinalists are announced in advance and then a competition decides the winner, should bring new attention to the Prizes"

The announcement represents an agreement between the many institutions involved in awarding the Nobel Prizes including the Royal Swedish Academy of Sciences that presides over the prizes in Chemistry, Physics and Economics; the Nobel Assembly at the Karolinska which awards the Prize in Medicine, the Swedish Academy which awards the Literature prize and the Norwegian Nobel Committee that awards the Peace Prize.

At the press conference, the Nobel Foundation presented the new reality series, one for each Nobel Prize. The example they highlighted relates to this years prize in Physiology and Medicine which will be given out via "Nobel Survivor." This show will feature Nobel Semifinalists living on a remote tropical island and the competitions will feature major medical "events" that one member of each team will experience.  Each week the team that responds least well to the challenge will have to vote off one member.  The challenges will include infections by schistosomes and filarial nematodes, a series of autoimmune disorders, premature aging, erectile disfunction, and severe body odor.  The competitions will be presided over by Hugh Laurie.

"Many of the Physiology and Medicine prizes have been criticized for being too disconnected from actual Medicine.  So we figured what better way to pick the winner than to make them actually do some medicine, but without all the comforts of home," said Barbara Connon. This years semifinalists who will be participating include J. Craig Venter, Lee Hood, Joan Steitz, Alec Jeffreys, Carl Woese, Norm Pace, Mary Claire King, Douglas Coleman, Elaine Fuchs, and James Till.

Other shows for this and future year's prizes include:

Sweden's Next Model (System)
The 2011 Medicine and Physiology prize will feature a competition to determine what is the best model organism.

Real Literature Idol
The 2010 Nobel Prize in Literature will be given out via a literature reading and slam poetry series dubbed "Real Literature Idol"

The Amazing Particle Race
The 2010 Nobel Prize in Physics will be given out to the scientist who is best able to maneuver their particle through a month long journey around the globe.

Dancing Peacefully With the Stars
Enough with Peace Prizes being given to people who work on abstract global issues.  The 2010 Nobel Peace Prize will be given out through a dance competition.  All "stars" selected for the competition will be notorious for their difficulty in getting along with others and will include Mel Gibson, Alex Rodriguez, Lindsay Lohan, Barbara Streisand, Kanye West, Dick Cheney, Amy Winehouse, and Courtney Love.

The Swedish Chef
In order to make chemistry more "Real" for the public, the 2010 Nobel Prize in Chemistry will be awarded in a Swedish Cooking competition.

The Nobel Apprentice
The Prize in Economic Sciences (though not technically a formal Nobel Prize) will be awarded via a collaboration with an existing reality show "The Apprentice." Candidates for the prize will compete to be Donald Trumps economic advisor.

The Nobel Foundation is also soliciting feedback, right here on this blog, for ideas for other Nobel Prize related reality shows for future awards.  Please submit suggestions.

Tuesday, September 28, 2010

So crappy it is awesome: Paper from Poo

Well, here is one for you microbiome fans out there.  Went to the UC Davis Vet School store on the way to work and found a display selling Paper from Poo. Not human poo of course but from animals that have a lot of fiber in their diet, like pandas, cows, horses and elephants. Some of the slogans are great such as:

"We take the 'OO' out of Poo!"

"We're number one at number two"

Here are some pics of the display:



For more on this see the PooPooPaper website.

Monday, September 27, 2010

BIS002C "Biodiversity & the tree of life" Lecture2&3 more on phylogeny & trees

Well, tomorrow is going to be a bit crazy for me.  I teach four lectures tomorrow for "BIS002C - Biodiversity and the Tree of Life" and UC Davis.  Well, actually, I do each of two lectures twice.  This happens for two reasons.  First, there are two sections for the class and the way we do it, each faculty gives each lecture for which they are responsible twice.  Second, on Mondays, we do two lectures for each section.  In total there are four lectures per week and our schedule is as follows

Section A:  MWF 11-12 M 6-7
Section B: MWF 3-4 M 7-8

So tomorrow at 11 AM I give Lecture 2 for the class to Section A.  Then at 3 PM I give Lecture 2 to Section B.  Then at 6 PM I give Lecture 3 to Section A.  Then at 7 PM I give Lecture 3 to Section B.  Well, enough trying to make it seem like I am working hard.  Especially after PZ Myers gave me a little grief about this on twitter since, well, my teaching load is not actually that big compared to many.

Anyway - back to the class.  I am going to be posting about the class here as much as I can.  To give people an idea of the whole course this is the general highly simplified schema:

Lectures 1-5 Phylogeny (me)
Lectures 6-13 Microbes (Bacteria, Archaea, microbial euks) (me)
Lectures 14-21 Plants and relatives (Jim Doyle)
Lectures 22-24 Fungi  (Jim Doyle)
Lectures 25-36 Metazoa (Susan Keen)
Lectures 37-38 Wrap up, symbioses, etc (Susan Keen)

I do Lectures 1-13 and possibly 37-38.

For the first week or so I am introducing the students to various aspects of phylogeny and phylogenetic trees.  We do this in part because the rest of the class is oriented around using phylogenies and phylogenetic trees so it is important that the students really understand them.

To that end, tomorrow here is the plan:

Lecture 2 will focus on (a) the components of a phylogenetic tree and what they mean plus (b) taxa and groups in trees.  Among the topics we will cover are rooted trees, rotating trees (e.g., vertical vs. horizontal), rotating branches in trees, monophyletic groups/clades, non monophyletic groupings, outgroups vs. ingroups and more.  Oh in addition we will show the awesome Tree of Life movie that we did not get to on Friday. See below




Lecture 3 will then focus on characters and on tracing character evolution on trees.  Among the topics we will cover include traits vs states, homology, ancestral vs. derived, synapomorphies, and the many faces of homoplasy.  Am planning to start posting slides from the class after lecture hopefully starting soon.  But I keep refining them so not going to post before I am close to done ....

Any comments or suggestions welcome ...

Thursday, September 23, 2010

BIS002C "Biodiversity & the tree of life" Lecture 1 tomorrow: Intro to phylogeny; #UCDavis

Well, tomorrow begins some serious craziness here at UC Davis for me.  School started today for the Fall Quarter here and tomorrow a class I am co-teaching (with Jim Doyle and Susan Keen) has its first lecture.  The course is labelled BIS002 C "Introduction to Biology".  It is the third class in a three course/three quarter series.  BIS 002A covers molecular and cellular biology, genetics and related topics (just lecture).  BIS 002B covers the principles of ecology and evolution (with a lab).  And BIS 002C covers "Biodiversity and the Tree of Life" (also with a lab).

A few things to note.  First, each of these courses has to get taught each quarter here, since so many students major in or do something related to life sciences here at Davis.  And on top of this, each course has some 6-700 students (or more).  Alas, since we do not have a lecture hall big enough for this number of students, we have to give each lecture twice.  This means that, for BIS 002C which I only teach a little over a third of, I end up giving 24 lectures over three weeks (2 sections x 4 lectures per week per section = 8 lectures / week).  It is a bit crazy shall we say.  But fun too.  In total, some 2500+ students go through the series per year.

So, tomorrow it begins for me for 3+ weeks of intensity.  But I look forward to it I guess each year since the topics I cover I hold near and dear to my heart.  For the first week of the class, I will introduce the students to phylogeny (what is it, what are phylogenetic trees, how do we infer them, how do we use them).  Then I spend two whole weeks discussing microbial diversity - phylogenetic and functional.  I view this as a privilege in many ways as it is somewhat unusual for 8 lectures to be used in an introductory course on microbial diversity.

Anyway, I will be posting here some comments and details about the class and I thought I would give this tiny introduction.  Tomorrow we will spend some time introducing the course and discussing practical details and then I will get 20-30 minutes to introduce students to phylogenetic trees.  The whole series currently uses as a textbook "Life: The Science of Biology, 8th Edition" by Sadava et al (we are switching over to the 9th edition but not for this quarter) and for class I try to use as many figures from the text as possible.  But I also mix in my own here and there.

Here is an outline for tomorrow after the course intro

1. Introduction to biodiversity of life
2. Discussion of phylogeny
   * Definition
   * Show a few trees
3. Discuss how trees are oversimplifications of true evolutionary history but are useful
   * Populations not shown
   * Not all lineages shown
   * Complication of reticulation/gene transfer
4. Describe different components to a tree
5. Walk through the course outline using a tree of life as a guide
6. 3-4 examples of uses of phylogenetic trees
7. If time permits show a little movie (see below)

Wednesday, September 22, 2010

Quick Tip: if you want someone to share job ads, announcements, etc, send links to web sites not attachments

OK I have had it. I have had it with people who send me job ads and meeting announcements and other things they want me to "share" with colleagues or students. I got six such requests today - two for job ads, two for course announcements and two for meeting announcements.

But this rant may not be what you think. I am not annoyed that they want me to share something. I actually like doing this. What I am annoyed with is how people do this. 95% of the time people send these email requests with an attachment and expect me to forward this on to all who might be interested. And much of the time these attachments are big files, sometimes written in programs that only some people can open.

Does this work some of the time? Sure. Do I sometimes forward these on? Sure. But that approach is so 2005. Here in 2010 there are better ways than email blasts to people who mostly just click delete. In my opinion, the best way to get someone to share something like this is to post your announcement on the web somewhere and then send people a link to the web site. Include a brief summary in the email you send around and if people want more information they can go to the web site. Not only does this save some bandwidth and not clutter up peoples email servers, but it also allows those of us who share via Twitter and Friendfeed and Facebook and so on to more easily send the announcement around. I am sure many people prefer the attachments, but I for one get 50+ attachments a day, almost all of which do not get looked at.

UPDATE 9/23/2012
So - the post above was written two years ago, almost to the day.  And not much has changed.  Excepted perhaps the way people share links (I mention Friendfeed above --- I guess I that could be replaced by Google+).

What is an easy way to post a document and then send people a link?  There are many ways to do this including

  • Post as a Google Doc/Presentation in Google Drive and send the link
  • Upload to Dropbox or another such site and, well, share the link
  • Post as a blog post (if you have a blog) or friggin start a blog and post it there
And of course many many other ways.  But please please please stop sending all these files around.  For a while I was posting them to my blog (I can autopost by forwarding email messages to the right address).  But I am sick of doing this for other people and am going to stop.

Sunday, September 19, 2010

Probiotic use spreading, lots of money being made, known benefits still murky

A little news report from last week prompted me to write this mini post.  The report (Global probiotics market approaching $30bn by 2015: Report) indicates that the use (and purchase) of probiotics is spreading globally.

I find the whole thing pretty interesting actually. I personally think that at some point we will be able to figure out how to use "good" microbes to manipulate and manage human health and performance in all sorts of ways.  And there is more and more evidence that in some cases probiotics can have positive effects.  So in a way it is not surprising that more and more people are buying and using probiotics.

On the other hand, the evidence showing that probiotics are actually beneficial is still limited.  I note, this is why I have started giving out an "Overselling the microbiome and probiotics award" here.  So far, the best simple site I have found discussing probiotics is from NCCAM - the National Center for Complementary and Alternative Medicine.  This may come as a surprise to some (as it did to me), since NCCAM has been severely criticized by many for its support of pseudoscience (e.g., see here).  I note I am not even remotely trying to defend much of what NCCAM does here.  I am simply pointing out that they have a decent resource on probiotics.

For more on the science of probiotics see "Probiotic Microbes: The Scientific Basis" from ASM.  The report references above clearly seems to overstate the potential of probiotics by suggesting that they are being targeted for use in all sorts of health situations without presenting the caveats that these health benefits are not that well established.

Anyway, given that the evidence for benefits of probiotics is still pretty sparse, the fact that their use is spreading very rapidly is I guess a little bit disconcerting.  I would be willing to wager that a lot of the spread has to do with deceptive marketing practices by probiotic suppliers.  But there is a silver lining to this.  I think over the next few years we will see many new discoveries relating to where and when probiotics can help people and animals and such.  And the fact that the notion of "good microbes" is spreading is a good thing since we certainly need to reduce the "kill all microbes" mentality that has pervaded in some circles (consider the use of antibiotics in all sorts of materials).

Anyway, just a little post here about the spread of probiotic purchasing.  One thing I will end with - the report referenced above mentions that probiotics are being put into all sorts of new foods including "chocolates, cheese, muffins, and sausages".

Sunday, September 12, 2010

Lake Arrowhead Microbial Genomes notes, live streaming, I hope here, #LAMG10

Will be posting to Twitter notes on the Lake Arrowhead Microbial Genomes Meeting and am experimenting with FriendFeed and other embedding here. Hope this works for those not using Twitter.





Probiotics are the new viagra & the risks of overselling of probiotics

For crap's sake.  Really.  This is for crap's sake.  I have been sniffing around the web looking into stories about probiotics and, well, it is scary.  So much of the stuff out there is so incredibly awful.  There are so many sites out there offering probiotics for sale it reminds me of viagra.  But in a way this is way worse, because at least viagra sales only really offer to cure one kind of ailment.  Probiotics offer to cure everything under the sun.  And more.  And along with these offer's to cure everything come some seriously worrying practices.

Take for example this press release: New Website Offers Analysis On Top Probiotic Supplements.  This new website is "BestProbioticReviews.Com" and it portrays itself as some sort of neutral party.
BestProbioticReviews.com is a comprehensive yet easy-to-read guide offering product reviews on the top 3 probiotic supplements on the market today. Learn more about the best probiotic supplements and their review today.
They go on to report that
Based on the tests performed, the best probiotic supplement that has achieved the highest possible rating is Nutraelle DigestiveCare. The probiotic supplement received high marks because it was said to help consumers improve their overall digestive health, immune defense, and little to no side effects.
And follow this with
Of course, BestProbioticReviews.com wasn’t set out to provide just product information. We’ve included a special section outside of digestive health and showed our readers’ probiotics help in many ways other than just inside the gut. We discuss how probiotics in general can help (http://www.bestprobioticreviews.com/probiotics-IBS.html) probiotics IBS relief, bacterial vaginosis, yeast infections, and respiratory health problems like asthma.
So - they first imply they are neutral.  Then they tell you about the small benefits of probiotics and then go on to discuss how probiotics can help with lots of other ailments.  And then they link out to sites for buying the three different kinds of probiotics they recommend.  The #1 recommended priobiotic is something called Nutraelle which apparently has all sorts of benefits, though the * tells us none are supported by the FDA.

Anyone want to bet that this web site is actually somehow affiliated with one or all of the places it recommends?  Interestingly, if you look at who is running this site it says it is:

Kelly Moore
Best Probiotic Reviews.com
815 1st Avenue
Seattle, Washington 98104
(206) 624-3313

A little snooping around finds a press release from the same phone number for Alpranax - a claimed anti anxiety med.  The web site for this med has some striking similarities to the one for the probiotic promoted by Kelly Moore.

And alas, looking around the web for people selling probiotics, it really is starting to resemble those selling erectile disfunction treatments or various other therapies. Now mind you, I am not saying here that probiotics do not have potential.  They have been shown, here and there, to have positive benefits for a variety of ailments.  But I am going to repeat something here I have been posting every once in a while:
For the statement "X manipulations of microbes help treat X ailments in X people X of the time": X="some" NOT "all"
Or, in other words, the few studies that have been done on probiotics have shown that they can be effective in some people some of the time to treat some ailments.  But extending this concept to all probiotics help treat all people all of the time for (all or many) ailments is ridiculous. And alas, that is what some supporters of probiotics are doing.

For fun, here are some links discussing some issues with claims about probiotics

Here is some interesting reading relating to the potential for government regulation of claims about probiotics:

I hate to see more regulation by the government without justification.  But I am starting to wonder here if some more stringent regulation may be needed here.

Personally, I think probiotics have a lot of potential.  And more and more scientific studies are telling us where that potential is, and where it is not. But this risks getting lost in the midst of overselling, scams, and deceptive practices.  Here's hoping evidence becomes more a part of the culture (pun intended) here.  

Friday, September 10, 2010

Searching twitter for science related topics; best strategies? favorite searches?

I have been experimenting with different twitter searches relating to genomics, microbiology, evolution, and other work things and find it actually somewhat fascinating.  The key thing has been to try and find searches that pull out useful / interesting stuff but not crap.  For some topics, this is easy, like microbiome and metagenomics.  These work well for a few reasons I think including that they are technical but used somewhat commonly within the fields in which I am interested.

You can try to get a bit more specific with them if you look for the hashtag version of these words: #microbiome and #metagenomics.  This works OK for #microbiome but #metagenomics yields nothing right now.

Unfortunately, some potentially useful terms have been coopted by all sorts of non-interesting stuff. Consider evolution and bacteria, for example.  In these cases, the words are too commonly used either for non sciency stuff (e.g., evolution of skateboards just came up) or for non interesting stuff (e.g., kitchen cleaners come up a lot with the bacteria search).  In these cases, the hashtag versions are better though imperfect: #evolution and #bacteria.

The key seems to be to find terms that are used somewhat narrowly to be only about the topic you care about but are also used widely enough so that a lot of people in the field of interest use them.

Here are some of my current favorite/most useful search terms:

If you want, you can always go beyond these and do more advanced searches.  But I tend to stick to the simple ones much of the time.  I know many people do all their searching within twitter clients, and each has their own flavors of options, but for a few reasons I prefer to do searching directly at the twitter site.   


I continue to experiment with different approaches to this and would welcome any ideas for best ways to pull out useful material. 

Also, I am curious.  Do others out there who use twitter have some favorite terms they search for?

Wednesday, September 08, 2010

Blog sponsorship spam - no thanks; wonder if this is how Pepsigate started?

Got this one today (see below).  Been nice knowing everyone.  Will be getting rich soon and will drop this blog like a stone.
Hi my name is Taj Jones and I'm a blog spotter. I basically scour popular blogs in an effort to find great writers. I loved your post on A complete summary, nice job!

I'd like to get straight to the point.

Our client wants people like you to sponsor their products and will pay you to do so.

They're launching an educational product on September 7th that teaches others how to make money on the internet by using Facebook and Social Media.

We want to pay you for recommending that product to your loyal blog readers and we will pay you up to $200 for each person that you refer. If you make just one sale a day you're looking at making around $6000 per month.

All you need to do is create a few blog posts that recommend this product. You may also use one of our nice banners and place it on your blog.

It's pretty simple, takes very little time (10 minutes or so) and will be very rewarding.

All sales that you refer are tracked through your own special link and you will get paid every week. Payments are always on time and will be sent to you via Check.

This deal is totally legitimate and we will NEVER ask you for any fee, or to sign any contracts.

What do you need to do if you are interested?

I have more details, a video and instructions for you here:

(Sorry all, I am not posting the link)

Regards,

Taj Jones

Tuesday, September 07, 2010

More of the worst conference descriptions ever

Well, I got invited to another conference that is brought to you by the same people who brought us what I thought was possibly the worst conference ever: Science Conference SPAM: ICEME2011 on all of engineering & metaengineering.  But amazingly this one is just as bad.  Well, actually, these ones - it is two conferences. See http://www.iiis2011.org/imcic/website/default.asp?vc=28 and http://www.iiis2011.org/imcic/website/default.asp?vc=3. I guess I could show you the title of the conference but the web address is informative.  I would bet that some other numbers at the end end up being used for other conferences.

Anyway see the letter at the end of this post - it is very similar to the one for the ICEME meeting.  The best part is when one goes to the "About the conference" sections.  For example see here
CCCT 2011 is an International Conference that will bring together researchers, developers, practitioners, consultants and users of Computer, Communications and Control Technologies, with the aim to serve as a forum to present current and future work, solutions and problems in these fields, as well as in the relationships among them. Consequently, efforts will be done in order to promote and to foster the analogical thinking required by the Systems Approach for interdisciplinary cross-fertilization, "epistemic things" generation and "technical objects" production.

Can't wait for this meeting on Microbial Communities as Drivers of Ecosystem Complexity

I truly can't wait for this meeting: Keystone Symposia Conference | Microbial Communities as Drivers of Ecosystem Complexity - Program

Organizers: Jacques Ravel, Vincent B. Young, Mitchell Sogin and Trina McMahon. March 25 - 30, 2011 • Beaver Run Resort  •  Breckenridge, Colorado

The current program is listed below.  Still time to register.  Oh, and it is in Breckenridge, CO, which is kind of nice.  If you are interested in microbial communities, especially molecular studies of said communities, this could be the place to be ...
  • Norman R. Pace, University of Colorado at Boulder, USA 
    Molecular Analysis of Microbial Communities - Historical Perspective
  • Mitchell Sogin, Marine Biological Laboratory, USA Long-Tailed Microbial Communities
  • Susan Lynch, University of California, San Francisco, USA Microbial Community Analysis Using the PhyloChip
  • Jonathan A. Eisen, University of California, Davis, USA Phylogenetic and Phylogenomic Approaches to Metagenomic Analysis
  • Joseph Petrosino, Baylor College of Medicine, USA Sequencing Technologies Applied to Studying Microbial Ecology
  • Patrick D. Schloss, University of Michigan, USA Developing and Validating Tools for Computational Microbial Ecology
  • Rob Knight, University of Colorado, USA Quantitative Insights into Microbial Ecology
  • Jed Alan Fuhrman, University of Southern California, USA Integrating Molecular and Environmental Data to Evaluate Community Patterns
  • John Heidelberg, University of Southern California, USA Metagenomic Analysis of Marine Microbial Communities
  • Peter J. Turnbaugh, Harvard University, USA Metagenomic Analysis of the Human Gut
  • Susannah Tringe, DOE Joint Genome Institute, USA Bioenergy Metagenomics
  • Stanislav Dusko Ehrlich, Institut National de la Recherche Agronomique (INRA), France A Human Gut Microbial Gene Catalogue Established by Metagenomic Sequencing
  • Trina McMahon, University of Wisconsin-Madison, USA Functional Genomics of Polyphosphate Accumulating Bacteria: 'Eco-Systems' Biology for Wastewater Treatment
  • Gregory J. Dick, University of Michigan, USA Talk Title to be Determined
  • Robert L. Hettich, Oak Ridge National Laboratory, USA A Proteogenomic Approach for Characterizing the Molecular Activities of Gut Microbiomes
  • Brendan Bohannon†, University of Oregon, USA Environmental Microbial Ecology
  • Claire Horner-Devine, University of Washington, USA Biogeography of Microbial Communities
  • Thomas Schmidt, Michigan State University, USA Ecologic Strategies of Environmental Microbes
  • Margaret Riley, University of Massachusetts Amherst, USA Antibiotic-Induced Changes in the GI
  • Jacques Ravel, University of Maryland School of Medicine, USA The Temporal Dynamics of the Vaginal Microbiota
  • Forest Rohwer, San Diego State University, USA RNA Virus Communities Associated with Human
  • Zoe G. Cardon, Marine Biological Laboratory, USA Soil Microbial Ecology
  • David A. Stahl, University of Washington, USA Metabolic Modeling of a Mutualistic Microbial Community
  • Jay P. Tiesman, Procter & Gamble, USA Microbial Community Analysis from a Systems Biology Perspective
  • Edward F. Delong, Massachusetts Institute of Technology, USA Systems Biology of Planktonic Marine Microbial Communities
  • David A. Relman, Stanford University, USA Perturbation of the Human Microbiome: Unrest at Home
  • Julie Segre, NHGRI, National Institutes of Health, USA The Skin Microbiome
  • Vincent B. Young, University of Michigan, USA Integrating Human Microbial Ecology in a Clinical Setting

Irresponsible reporting on "poop doping" from the Washington Post

UPDATE - see below - the author updated her article including some of my critiques. Went on a bit of a Twitter tirade last night. See mor...