Author: Jonathan Eisen

I am an evolutionary biologist and a Professor at U. C. Davis. (see my lab site here). My research focuses on the origin of novelty (how new processes and functions originate). To study this I focus on sequencing and analyzing genomes of organisms, especially microbes and using phylogenomic analysis

A badomics word for good purposes: new paper on the "ridiculome"

Quick post here.  There is a new paper in BMC Biology which uses a bad omics word in the paper and in the title: BMC Biology | Full text | Logic modeling and the ridiculome under the rug.  Fortunately they are using the term to poke a bit of fun at people who think genomics will solve all of their research problems.

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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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A scientific study of gender bias in scientific conferences: new #PLoS One paper from #UCDavis

Well, this is certainly very interesting especially given my recent obsession with gender biases in scientific conferences (e.g., see The Tree of Life: Q-Bio conference in Hawaii, bring your surfboard and your Y chromosome because they don’t take a XX) ….  A press release from UC Davis (see here: Science, still a man’s world? (VIDEO) :: UC Davis News & Information) describes a newly published study on gender bias in science conferences.  The study was published in PLoS One a few days ago:

Isbell LA, Young TP, Harcourt AH (2012) Stag Parties Linger: Continued Gender Bias in a Female-Rich Scientific Discipline. PLoS ONE 7(11): e49682. doi:10.1371/journal.pone.0049682

The most disturbing piece of data is shows in Figure 2

Figure 2. Proportion of women as first authors of posters, talks, and symposia at AAPA meetings. The average proportion for all presentations with women as first authors over a 21-year period of annual meetings of the American Association of Physical Anthropologists is indicated by the solid black line. F-Org. Symp.: symposia organized by women only; F/M Org. Symp.: symposia organized jointly by women and men; M-Org. Symp.: symposia organized by men only.. 

So this seems to suggest that when men organize conferences women are much more underrepresented than they could / should be based on #s in the field. Similar to my observations in certain areas.

Some other things I have written on this 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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A call, on Thanksgiving, for unrestricted References and Acknowledgements sections for papers

On this Thanksgiving 2012 I am calling for a change in the way we acknowledge the contributions of others to our academic work.  We all stand upon the shoulders of those who have come before us.  And in the digital age we have the power to track much more completely what prior work has contributed to ours and also what people have helped along the way who are not reflected in author lists.  It is time for journals to do more to record these contributions.  So I am making a call here for a few simple things we can all do in this regard:

1. Reference EVERYTHING you can in your works if it is relevant.  
Use a computer program for some of your work?  Make sure you cite the program in some way.  Use some data as a key part of your analyses?  Cite the source of the data.  (For example, in my area people are really bad about citing genome data).  Got an idea from some paper about how to do an analysis?  Cite that paper.  I find it absurd that some journals arbitrarily restrict the number of citations one can use in a paper.  Sure, don’t overcite things that are trivial.  Don’t overcite yourself either.  But cite everything that matters.
2. Write complete and detailed Acknowledgement sections.  
Describe in as much detail as possible whomever contributed in some way to the work.  Sure, in printed papers a long Acknowledgement section may be a bit much.  But this is the web era.  Many journals already have online methods sections that are longer than those in the printed version.  It is time to do the same thing for Acknowledgements.  
3. Annotate in detail the contributions of authors on a paper.  
Most journals (at least in the sciences) now have a section on “Author’s Contributions” although some of them have arbitrary categories one is supposed to use.  Don’t follow those silly categories.  Write a section that details what authors ACTUALLY did and put it in your paper.  Many journals will allow one to replace the arbitrary categories with one’s own text.  
It is by detailing the actual contributions to one’s work that we can really show the spirit of Thanksgiving in academic work. 
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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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American Gut Project: Food, crowd sourcing, citizen science, open science, and MICROBES – what could be better?

A press release just came out announcing the American Gut Project: New public gut bacteria study expected to reach around world | University of Colorado Boulder.  From Rob Knight, Jeff Leach and others this project aims to engage the public in a large scale study of the connection between diet and the human gut microbiome.  Read more about it in the press release and I am sure more will come out soon.  Full disclosure – I have agreed to be a collaborator on the project – though as a fully open project I think pretty much anyone could be a collaborator.  Anyone this is definitely worth checking out.

As an aside – this is not the only crowd sourcing microbiome project out there.  I just became aware of another one called uBiome and I am working on getting a guest blog post from the organizers.  The American Gut project has got dozens of the major players in microbiome research involved.  And with Rob Knight being one of the key players one can expect it to big, cutting edge things.  Not sure about the scope / plans of uBiome but hopefully we will find out more soon.

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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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Thank you Google Scholar Updates for finding me two new papers to read

Am really liking the Google Scholar Updates system.   Have written about it before: The Tree of Life: Wow – Google Scholar “Updates” a big step forward … and continue to be impressed.  Today the system suggested two papers for me

Dead on accurate in terms of papers I would be interest in.  #1 is on Drosophila associated microbes and it is a paper from Dmitri Petrov’s group: Bacterial diversity associated with Drosophila in the laboratory and in the natural environment.  #2 is on computational normalization of shotgun genome sequence data from Titus Brown and others.  As these are both preprints I almost certainly never would have found them without Google Scholar Updates.

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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 evil germy pacifier story is getting out of hand – w/ Dr. Glass misleading the charge

From Wikipedia

Oh for crying out loud.  This is getting out of control.  Two weeks ago I wrote about an over the top story in US News and World Report about pacifiers and microbes: The Tree of Life: Germophobia 101: there are microbes on pacifiers ….  The culprit in this story was a Dr. – Dr. Tom Glass – who was the lead presenter of some study at a meeting.  His study involved counting the number of colony forming units on used vs. new pacifiers.  And low and behold used ones were covered in germs.  Amazingly, this led Glass to say ridiculous things like

In the long run, it may be that what you do now [using a pacifier] may have a lot to do with whether a child ends up developing atherosclerosis or type 2 diabetes.

Completely misleading and deceptive and dangerous I would say.  And alas, the story has been crawling it’s way around the web picking up speed.  Now it is at Time.Com with another story about Glass’ work: Bacteria on Binkies: A Recipe for Crankiness | TIME.com.  Glass apparently is now blaming biofilms of pacifiers for all the problems.  And again Dr. Glass is (mis)leading the charge against pacifiers.

A lot of times when a child is cranky, the first thing a parent does is reach for a pacifier,” says Dr. R. Tom Glass, the study’s principal investigator and a professor of forensic sciences, pathology and dental medicine at Oklahoma State University. “But what are you using to treat the crankiness? It’s a vicious cycle.

and

“biofilms can potentially increase the likelihood of colic or ear infections and could possibly heighten the risk of allergies or asthma, says Glass.”

The reporter does present some skepticism from parents and from the literature.  But come one – why even report this crap from Glass.  I mean – I am all for keeping babies from getting sick and pacifiers very well may be a source of some nasties.  But let’s think about the big picture here.  Parents buy pacifier.  Parents open package.  Parents give to baby.  Baby puts in mouth.  Baby drops pacifier and it gets dirt on it as well as some germs.  Baby puts back in mouth.  Pacifier gets left on counter.  Things from babies mouth grow on pacifier.  Baby puts pacifier back in mouth.  And so on.  Tell me again where the pacifier introduces bad germs to this system?

UPDATE: some reading material

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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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My new microbe art corner w/ three works by @artologica

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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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Must read microbiome paper of the month: defined microbioata treatment of Cdiff infections

This is a must read: PLOS Pathogens: Targeted Restoration of the Intestinal Microbiota with a Simple, Defined Bacteriotherapy Resolves Relapsing Clostridium difficile Disease in Mice

This is the paper I referred to in a previous post: Mouse study of fecal transplants to treat Cdiff infection.  This post was about a BBC News story that appeared to have jumped the embargo.  And then the news article disappeared and the scientific article was missing.  Thankfully the paper is now out.

The article has gotten some press that was not retracted.

More on fecal transplants and bacteriotherapy from my blog can be found below:

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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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Microbes, art and a bit of satire all in one place – Design Interactions at the RCA

Got pointed to an interesting site recently – “Design Interactions at the RCA”  This is a program (or as they call it – a programme) at the Royal College of Art in London.  One of the current students – Lana Porter – contacted me about a possible project she was working on involving microbes.  She also pointed me to some past projects connected to microbes from the program.  The two she pointed to are:

  • Viruses, close enemies or distant cousins? | Design Interactions at the RCA. From Mikael Metthey.  It appears to be from a few years ago but I am not sure.  Regardless, it is pretty humorous.  It is basically a description of an attempt to create “more intimate ways to approach the process of vaccination” by having poxteddy bears and cowpox rides and vaccination playgrounds.
  • The Race.  From Michael Burton.  Also from a few years ago. This one is about antibiotics and microbial evolution and the hygiene hypothesis.  

And then browsing around the site led to some other interesting concepts:

Seems like a fun programme (or program) …
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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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RISE Symposium

Just received this:

2012-Nov-30-RISE-Symposium.pdf
Inaugural RISE Symposium Agenda.pdf