Eisen Lab Blog

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

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

I note I do not think Woese should win a Nobel for discovering the archaea.  That was a groundbreaking finding but it does not fit well with the Nobel Prize categories.  I think he should win it for the concept of molecular classification of microorganisms and applying this in general to the microbial world around us.  This concept (expanded by Norm Pace and colleagues to uncultured microbes) revolutionized our approach to studying single microbes in the environment, to studying single microbes infecting people and to studying communities of microbes in and on people.  And thus Woese and Pace in my opinion deserve the Nobel Prize for Medicine.  I will be expanding on this in a future post …
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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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News from microBEnet

Coming soon

American Chemical Society not winning any blogging friends these days

Wow – just got an email from a colleague with details on a scientific publishing saga.  Here is the summary:

Stage 1: Jenica Rogers wrote a blog post expressing a bit of frustration with the American Chemical Society and their publishing system: Walking away from the American Chemical Society

Stage 2: The Chronicle for Higher Education wrote a story about it: As Chemistry Journals’ Prices Rise, A Librarian Just Says No

Stage 3: The Director of Public Affairs for the ACS responded to questions and was quoted with the following

“We find little constructive dialogue can be had on blogs and other listservs where logic, balance and common courtesy are not practiced and observed,” Glenn S. Ruskin, the group’s director of public affairs, said in an e-mail message. “As a matter of practice, ACS finds that direct engagement via telephone or face-to-face with individuals expressing concern over pricing or other related matters is the most productive means to finding common ground and resolution.”

Then he attempted to clarify some details of the quote in that he claimed that the following got left off the end of the quote “Therefore, we will not be offering any response  to this blog posting or the conversation that has ensued.” but when doing this he got a bit personal and nasty:

The individual responsible for the above cited blog certainly has the right to her opinion, but that does not excuse rude behavior or her use of profanity and vulgarity in addressing ACS or its employees. While not evident in the most recent postings, I won’t repeat what she has posted in the past.  But I think you would agree that vulgarity and profanity postings do not lend themselves to meaningful, productive and civil discourse, thus our decision not to engage any further with her on this topic

And the discussion continued on various blogs like Chembark.  The most disturbing part to me of the whole thing is that it is hard to find anything particularly extremely vulgar in writings by Jenica Rogers (I note – I only googled around for a minute or so so I may have missed things but Walk Walt at Random has more detail on this and also did not find any serious vulgarity).  Generally I find the response of ACS to be extremely distasteful.  They don’t like what she wrote.  So they go after her character.  Brilliant.

For other takes on this story see

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Headline says it all "Opera singer grows algae on her face by feeding it w/ her breath & then the audience eats it"

Wow.  I am always on the lookout for microbe-themed art.  In most cases, when I see such art, I think “wow – that is an interesting way of embedding microbes into a traditional form of art”.  You know – painting with microbes or art with microbes in it or such.  Well, in this new case I can say this is the most unusual and most creative use of microbes in art I have ever seen: Opera singer grows algae on her face by feeding it with her breath and then the audience eats it

You see, an opera singer work a “head-mounted, face-clinging device” which contained within in some algae in water.  And then the algae was fed by the opera singer’s breath.  This is part of something called the “Algae Opera“.  The most amazing part of this is described in the io9 article

“Because the algae’s growth is dependant on the amount of CO2 it receives, the singer controlled her pitch and volume to alter various characteristics of the algae, including taste (what they called “sonic enhancement”). Depending on the way she sang, the different pitches and frequencies could make the food taste either bitter or sweet”

And then at the end of the performances the audience was invited to sample some of the algae. Yum.  Certainly a bit weird.  But kudos on the creativity index.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Diabetes and the microbiome – some hype and some caution – in the same stories

A new paper is getting some press on a link between type II diabetes and the microbiome.  The paper is here.  The abstract of the paper reads:

Assessment and characterization of gut microbiota has become a major research area in human disease, including type 2 diabetes, the most prevalent endocrine disease worldwide. To carry out analysis on gut microbial content in patients with type 2 diabetes, we developed a protocol for a metagenome-wide association study (MGWAS) and undertook a two-stage MGWAS based on deep shotgun sequencing of the gut microbial DNA from 345 Chinese individuals. We identified and validated approximately 60,000 type-2-diabetes-associated markers and established the concept of a metagenomic linkage group, enabling taxonomic species-level analyses. MGWAS analysis showed that patients with type 2 diabetes were characterized by a moderate degree of gut microbial dysbiosis, a decrease in the abundance of some universal butyrate-producing bacteria and an increase in various opportunistic pathogens, as well as an enrichment of other microbial functions conferring sulphate reduction and oxidative stress resistance. An analysis of 23 additional individuals demonstrated that these gut microbial markers might be useful for classifying type 2 diabetes.

Seems pretty reasonable.  All they say there is that they found associations between bacteria and diabetes.  That is interesting but they do not seem to present any evidence about a causal connection.  Perhaps people who get type II diabetes end up then having their microbiome shift.  Perhaps a shift in the microbiome causes type II diabetes.  Or perhaps something else (e.g., excessive inflammation) causes both type II diabetes and microbiome shifts.  Who knows.

But alas a bit of hype crept into some of the the news stories.  And it seems that the scientists behind the study are responsible for some of this hype.  For example, consider the article Changes in Intestinal Bacteria Linked to Type 2 Diabetes – US News and World Report.  One quote is a bit much for me:

“I think our study provides many targets for disease prevention and treatment through gut microbiotia in the near future,” said study senior author Jun Wang, executive director of the Beijing Genomics Institute in Shenzhen, China.

Fortunately the reporter who wrote this story does a very good job of providing cautious interpretations.  See for example:

“There’s no way right now that you can say there’s a cause-and-effect relationship. It could be that the patients with diabetes were treated with drugs that changed their gut flora. Or maybe they ate differently? This is an interesting hypothesis — that gut bugs could influence diseases states — but it’s far from proven,” said Dr. Stuart Weinerman, associate chief of the division of endocrinology at North Shore University Hospital/Long Island Jewish Medical Center in New Hyde Park, N.Y.

Also see stories like Gut bacteria could cause diabetes from Science Codex.  The title alone makes me want to cry.  Some quotes as well as discussion in that article also seem, well, not cautious enough.

The research, which was recently published in the scientific journal Nature, also demonstrated that people with type 2 diabetes have a more hostile bacterial environment in their intestines, which can increase resistance to different medicines.

Definitely not buying this “hostile” environment claim.  Fortunately as with the US News story, there is some caution presented

“It is important to point out that our discovery demonstrates a correlation. The big question now is whether the changes in gut bacteria can affect the development of type 2 diabetes or whether the changes simply reflect that the person is suffering from type 2 diabetes.”

 So – the stories seem to actually be doing an OK job with the correlation vs. causation issue I have complained about many times.  And though some of the scientists may be pushing a bit of overinterpretation the reporters and even the press releases have some decent cautionary statements.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Fecal transplants in the news

CNN has a story on a fecal transplant case: Little-known fecal transplant cures woman’s bacterial infection – CNN.com.  It is worth a look and if you want to laugh (sometimes in pain, sometimes for jokes) read the comments. Some other recent stories on this topic include

And the CNN story got picked up by Reddit
As many know – I have been talking / writing about such treatments a bit recently.  I discussed it in my Tedmed talk (which is now on Ted).

http://video.ted.com/assets/player/swf/EmbedPlayer.swf And I have a blog post with background and links on the topic.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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The biggest academic scam ever (caution – attempt at humor here)

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Eisen Lab Paper.Li Magazine

Playing around with Paper.Li. Took feeds from the blogs and Twitter profiles of people in my lab. Seems to come out OK … http://widgets.paper.li/javascripts/sr.embeddable.js Paperli.PaperFrame.Show({ id: ‘6f0c6ad8-8b14-41e0-b46a-1a7592d3eadb’, width: 390, height: 480, background: ‘#ECECEC’, borderColor: ‘#DDDDDD’ })

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Fall 2012 C-DEBI Call for Proposals Deadline MONDAY 10/1/12

Forwarding this email to this blog:

Don’t forget! C-DEBI is interested in funding your research and education and outreach – with entrainment of new researchers not previously funded by C-DEBI as a major consideration! Proposals are due Monday 10/1/12.

Fall 2012 Calls For Our Research, Education and Outreach Grants are Now Posted! Apply now for C-DEBI funds in support of deep biosphere research, education and outreach. C-DEBI supports Small Research Grants and Small Education and Outreach Grants up to $50,000. C-DEBI also supports Fellowships for Graduate Students and Postdoctorals! Proposals are due October 1, 2012. See each opportunity for specific deadlines.

Lab meeting Sept 25th, 2012

Catherine Burke, from the University of Technology, Sydney will be presenting during our lab meeting this week.
We will be meeting from 1:30pm to 3:30pm at the Genome Center in room 4202.