Tony Rodriguez Illustration of Me for WiredUK

OK so I have not worn a tie in a very long time and I pretty much don’t wear a lab coat too often either but I totally love this:

// See the whole story here.

Twisted tree of life award #15: NBC News on "Junk DNA mystery"

Oh for fu$*# sake.  Really MSNBC?  I mean, I know perhaps I should not expect much from some in the press but this is just awful: ‘Junk’ DNA mystery solved: It’s not needed.

Brought to us by NBC News and LiveScience (which actually can have some pretty good science coverage).  This article has some complete and utter crap:

Some parts that I have issues with:

  • The headline: “‘Junk’ DNA mystery solved: It’s not needed.”  The headline is silly but alas it is consistent with what is in the article.
  • So-called junk DNA, the vast majority of the genome that doesn’t code for proteins“.  So – they have redefined junk DNA as all non coding DNA?
  • “For decades, scientists have known that the vast majority of the genome is made up of DNA that doesn’t seem to contain genes or turn genes on or off.”  Apparently there is an entity out there known as “The Genome”.  
And then we get into the quoting of author and researcher Victor Albert with no comments or responses from anyone is painful too.
  • At least for a plant, junk DNA really is just junk — it’s not required.”  Except that they did not show this – they just showed that one plant can have a small genome and not have a lot of “junk” as they call it, which of course does not really say anything about what “junk” does or does not do in other organisms.
  • Nobody’s really known what junk DNA does or doesn’t do” apparently calling into question the some 10,000 plus papers on the topic.

Apparently, from reading the rest the whole point of this article is that it turns out that people sequenced the genome of a bladderwort and it has a small genome but a lot of genes.  Oh and the organism is complex.  Therefore, apparently, it follows that

“The findings suggest junk DNA really isn’t needed for healthy plants — and that may also hold for other organisms, such as humans.”

And this leads us to ‘Junk’ DNA mystery solved: It’s not needed.



And for this evolutionary logic, I am awarding NBC News, Tia Ghose (the author of the piece) and Victor Albert, the 15th coveted Twisted Tree of Life Award.

Past winners:
UPDATE 5/17/13
Some other discussions of this paper and related to my critique (though not always agreeing with me)

Rosacea – What Causes It? News story overplays suggested connection to skin mites

Just got done reading this: Could Bacteria in Skin Mites Help Cause Rosacea? – US News and World Report.  The article leads off with a bold statement that caught my eye

“Bacteria carried by tiny mites on the skin might be responsible for the common dermatological condition known as rosacea, researchers say.”

This caught my attention because I have been reading up on skin microbes recently and though many have suggested connections between microbes and rosacea as far as I know nobody has shown any causal relationship.  And causation vs. correlation has been on my mind a lot recently.

So I read further and found some suggestive but inconclusive statements that were linked together

  • there are more of these mites on the skin of patients with rosacea than on those without
  • a bacterium (Bacillus oleronius) has been found in the mites and in people w/ rosacea
  • this bacterium can be killed with the same antibiotics that seem to have some success in treating rosacea
  • people with rosacea have an immune reaction to compounds from this bacterium 
  • another bacterium Staphylococcus epidermis also appears in patients w/ rosacea but not patients free of rosacea

And that apparently was it … not very convincing.  Sounds like just a lot of random correlations to me.  So I decided to dig deeper.  And I went to see fi I could find the paper which alas was not linked from the news story.

I googled the journal name “Journal of Medical Microbiology” and got to the web site.  The news article had said the “review paper” had come out August 30th so I clicked on the Papers In Press link and got to the paper.  I browsed the abstract, which seemed somewhat different from the gist of the news story

Rosacea is a common dermatological condition that predominantly affects the central regions of the face. Rosacea affects up to 3% of the world’s population and a number of subtypes are recognized. Rosacea can be treated with a variety of antibiotics (e.g. tetracycline or metronidazole) yet no role for bacteria or microbes in its aetiology has been conclusively established. The density of Demodex mites in the skin of rosacea patients is higher than in controls, suggesting a possible role for these mites in the induction of this condition. In addition, Bacillus oleronius, known to be sensitive to the antibiotics used to treat rosacea, has been isolated from a Demodex mite from a patient with papulopustular rosacea and a potential role for this bacterium in the induction of rosacea has been proposed. Staphylococcus epidermidis has been isolated predominantly from the pustules of rosacea patients but not from unaffected skin and may be transported around the face by Demodex mites. These findings raise the possibility that rosacea is fundamentally a bacterial disease resulting from the over proliferation of Demodex mites living in skin damaged as a result of adverse weathering, age or the production of sebum with an altered fatty acid content. This review surveys the literature relating to the role of Demodex mites and their associated bacteria in the induction and persistence of rosacea and highlights possible therapeutic options.

And then I did what usually causes me much anguish when I am at home – I clicked on the link for the full text, thinking that I would get a paywall.  And low and behold, I got the preprint of the paper.  The paper is quite interesting in many ways with lots of details about these mites I knew nothing about.  It also has a lot of detail on these two bacterial species and why the authors think they are of interest in rosacea etiology.  But no convincing evidence of any kind is presented that there is a causal connection to these bacteria or to these mites.  I leave everyone with the last paragraph of the paper

The pathogenic role of Demodex mites, as well as B. oleronius and S. epidermidis, in the induction and persistence of rosacea remains an unresolved issue. The lack of an immunological response to Demodex mites in healthy skin raises the possibility of localized immunosuppression, facilitating the survival of the mite. Hopefully, the results of further research will bring us closer to understanding the role of microbes in the pathogenesis of rosacea and assist in the development of new and more effective therapies for the treatment of this disfiguring disease.

I agree. Unresolved.

For those interested … storification of twitter discussion criticizing NY Times article on Venter cell model

Storification is here and below.[<a href=”” target=”_blank”>View the story “Critiques of NY Times story on Venter Cell Model” on Storify</a>]

Social Networks and Scientists: Chronicle for Higher Education Article

Quick post here.

There is a new article in the Chronicle for Higher Education in which I am quoted: Social Networks for Academics Proliferate, Despite Some Scholars’ Doubts

The article discusses many connected topics relating to the use of social media by scientists – though it does not make clear how everything is connected perhaps.  Anyway the author talked to me about Mendeley and various uses of Mendeley and I told her about an effort to create a Mendeley collection of my father’s papers.  The article also discussed LinkedIn, Academia.Edu, Twitter and other social media systems.

Some quotes

Jonathan A. Eisen, a professor of medical microbiology and immunology at the University of California at Davis, used Mendeley to distribute the research papers that his father, Howard J. Eisen, a researcher at the National Institutes of Health, published before he died, in 1987. After struggling to free papers locked behind pay walls, Jonathan Eisen compiled the articles and posted nearly all of them on a Mendeley page he had created for his father. 

Mr. Eisen, a self-described “obsessed open-access advocate,” described the impact in a blog post last year: “Thanks to the social features of Mendeley, more and more people will see and have access to those papers, thus ensuring that they do not wallow in never-never land but continue to have some potential impact on science and society.”

Perhaps most important from my point of view – I love the picture of me taken by Max Whittaker.

Jack Gilbert @gilbertjacka clarifies comments at #AAASMtg re: opening windows, cleanliness & microbes

Just got this to post from my college colleague Jack Gilbert in regard to some comments he made to the press at the AAAS Meeting a few days ago.  He sent this in part in response to some news stories that came out of the press conference we had at the meeting (e.g., see Florence Nightingale approach ‘could help fight infection in …Open hospital windows to stem spread of infections, says … and others).  And I encouraged him to consider whether or not he needed to clarify some of his comments – and here is his response.

A confession, lesson and retraction
By Jack A. Gilbert

At the AAAS 2012 annual meeting on Friday, I was involved in a press conference to announce the initial results and ideology for the Earth Microbiome Project ( Following the press conference we went to another room, where we were openly discussing these concepts with the reporters. Several reporters asked me to comment on the potential impact of this research in the medical sphere. At which point I started to discuss some excellent research by Jessica Green ( regarding her recent evidence that improved ventilation in hospital wards reduced the airborne abundance of organisms that were related to pathogens. I showed these reporters the paper
( and asked them to discuss this with Jessica Green.

I then proceeded to discuss some current research we are doing at University of Chicago that is looking at the impact of having a natural microbial community on surfaces to reduce the likelihood that pathogens can establish in that environment. Specifically we are exploring whether ‘good bacteria‘ can be used as a barrier to outcompete ‘bad bacteria’, I suggested that this was testing the hypothesis outlined by Florence Nightingale.

To this end I said, that maybe instead of sterilizing every surface in a hospital we could explore a different strategy. There is however currently only circumstantial evidence to support my claims, and I could have done a much better job in making clear that I was discussing an idea – not something for which there was evidence.

I am sorry for my indiscretion and hyperbole, and hope that I didn’t cause any groups or individuals concern or worry about this topic. These were concepts being discussed, specifically that by using the EMP we could explore ecological dynamics that could lay the groundwork to help determine if a community could play the role of a barrier against infection.

I want to stipulate that I believe hospitals should be cleaning, and I believe that surgeons should scrub and use the sterile method. To be clear, I wanted to state that ‘good’ bacteria could in the future play a role in reducing the instances of hospital borne infection, and that this is something we should investigate. People should wash their hands after the toilet, and wash their hands when they are sick; there is nothing wrong with being clean.

My science communication hero/heroine of the month – Dr. Kiki @drkiki

Been working on revising my lab’s web site and was looking for some videos of talks I have given online to post there.  And I discovered/rediscovered this video of an interview I did for Dr. Kiki’s Science Hour.  Here it is:


Now I know – this is over a year old. But I just watched the full video. Not so bad I think.

As many of you know, I like to talk.  And talk.  And talk.  But I would like to say that as an interviewer, Dr. Kiki is pretty frigging awesome.  Don’t know how she does it.  But I am going to post this video on the new lab page and point people to it if they want to know what my lab does and what I am interested in.

But enough about me.  I want to thank Dr. Kiki for this great interview by saying a little bit about her.  Or, well, her work in science communication.

As some of you may know, I listen to podcasts of TWIS – This Week in Science frequently on my bike rides to work.  And I really recommend anyone/everyone out there give it a whirl.  It is sort of like Science Friday but it is a bit edgier, a bit funnier, a bit goofier, and a bit sciencier (is that a word?)  Dr. Kiki and Justin on it are great and it is so good that I frequently sit outside my building listening to the end of a show if I take the short ride to work which is less than an hour.  So if you like Science – you really should check out the TWIS web site and find some way to listen such as what I do by subscribing to their podcasts at iTunes.

And I guess now I will be checking out “Dr. Kiki’s Science Hour” more after rewatching this video.  There are many many more shows at  I have not checked out as many as TWIS shows but the ones I have watched are great.

And if you want to follow her more directly check out her Blog: The Bird’s Brain, or her twitter feed  (@drkiki)  or her  Google+ feed.

Very proud that she is a UC Davis alum … and just want to say thanks to her for giving me a video I can share with others that says more about me and my lab than almost anything I have written.

Compiling a list of reporters who cover #microbiology stories well; suggestions wanted

Well, I got asked recently for examples of reporters who cover microbiology related stories well.  A few examples came to mind.

But before I biased anyone with those I thought I would snoop around the web and see if anyone else had written about this.  And in googling around I discovered something I probably should have known about – the American Society for Microbiology gives out a Microbiology Public Communication Award.  The list of past winners is very helpful. However, the ASM site does not have a lot of detail so I have tried to compile it here:

Year Recipient Highlighted story Publisher
2010 Debora MacKenzie An End to Flu? New Scientist
2009 Ken Armstrong, Michael Berens Culture of Resistance Seattle Times
2008 Martin Enserink, Leslie Roberts Combating Malaria Science Magazine
2007 Kenneth Weiss, Usha McFarling Altered Oceans Los Angeles Times
2006 David Baron, Clark Boyd, Katy Clark, Orlando de Guzman The Forgotten Plague: Malaria Public Radio International’s “The World”
2005 Leslie Roberts Polio: The Final Assault? Science Magazine
2004 Martin Enserink, Dennis Normile SARS In China Science Magazine
2003 John Fauber, Mark Johnson “A New Kind of Killer” and “The Hand of Man” Milwaukee Journal Sentinel
2002 Jonathon Knight Meet the Herod Bug Nature
2001 Janet Ginsburg Bio Invasion Business Week
2000 Susan Okie Science Races to Stem TB’s Threat The Washington Post
1999 Richard Monastersky The Rise of Life on Earth National Geographic
1998 Rachel Nowak, Ian Anderson Australia’s Giant Lab New Scientist
1997 Andy Coghlan Slime City: Where Bugs Build Skyscrapers New Scientist
1996 David Baro Living on Earth: Microbial Diversity National Public Radio

Obviously there are many other great journalists dealing with microbial topics out there. But this is a pretty interest list.  Most of the others I know about I know through their blogs.  Examples of reporters who’s microbiology writing I tend to like include:

There are also many microbiology bloggers out there who are great.  For now I am focusing on those who do more traditional reporting (e.g., writing for newspapers or magazines).   
So – I am now asking – do people have any other reporters who have done good work on microbiology related topics to recommend out there?  I am certain I am missing a few.

Some additional names coming from out there in the internets (with some links to example articles):

Arsenic revisited: discussing arsenic story with a #UCDavis biology writing class next week

Well, this could be fun. Next week I am making a guest appearance in a Writing class at UC Davis. The class focuses on writing in Biology and the instructor invited me to come in as a guest to coordinate a discussion of the arsenic paper and the coverage of it.
When the instructor asked for reading assignments I said they should read:

I think I probably should have suggested they read Zimmer’s excellent full write up here.  Going to suggest that now but may be too late.

Any other pointers to good write ups of what has happened since the first week after the paper would be appreciated.

Some suggestions coming in from twitter: