Eisen Lab Blog

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.

——–
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.

——–

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:

——–
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.

——–

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. 
——–
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.

——–

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.

——–
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.

——–

Water chemistry is hard

Well the theme of this week so far is summed up in the title here.  Because we know these coral ponds were going to be set up next week we ordered all of our kits and probes with expedited shipping… and they’ve been trickling in over a long period since.  We’ve been doing some initial experimentation with the measurements, but I’ll leave that story for the students.
Today we received colometric scanners that measure nitrate, nitrite, ammonia, phosphorus, and dissolved oxygen.  Only it turns out that it’s really only the scanners… they don’t actually come with the reagents required to use them.  Sort of like how the pH meter came on Monday with with instructions for activating and calibrating the electrode but none of those solutions either.

Any of course the day before Thanksgiving is clearly the best time to be putting in rush orders of reagents.  Not to mention the various things that still haven’t arrived and are about to get eaten by the holiday.

So… assuming everything gets here by early next week, and that we can get it all to work properly, and that we even have the right equipment to measure the levels we’ll encounter in the first place, we should be all set.

Another note on sampling

After discussions on sampling methods, we have decided on new samplings methods. Since we are getting rid of all 18 current samples, our new sampling methods will hopefully be consistent through out the whole project.

 

For the water samples, we will take 3 x 1.5 Liters of water in one Coral pond.

 

For the sediment samples, we want to take less than we have in the past. We plan to use 2 mL centrifuge tubes and fill them to the 1 mL mark. We will make sure to get a mix of oxic and anoxic layers of sediment.

 

For the wall scrapings, we will use a Kim wipe to vertically scrape up and down in one location on the inside of the container. We will put a piece of tape on the top of the container where we sampled, so we don’t sample there again (because there won’t be anything there after we scrape it off). This is important because we will be doing a substantial amount of sampling for our study on succession of the Coral ponds.

 

On a side note, we are also discussing whether we should sample from both coral ponds or just one. (They are identical in terms of maintenance and what is put into them) We haven’t come to a decision yet.

Thoughts on water chemistry kits and our current samples

Now that we have some of our new water chemistry equipment, we have discussed flaws in our first 18 samples. We collected all 18 samples with no tools to collect metadata (water chemistry). We have decided to take all the samples again and get rid of the 18 we already have. We still don’t have all the water chemistry equipment we need, but it should all be here tomorrow. It is crucial to determine the water chemistry at the time of every sampling. (During our study of succession on the coral ponds, this will be a lot of water chemistry testing!)

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.

——–
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.

——–

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

——–
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.

——–

Schedule for the new Coral ponds!

We have received a tentative schedule for the new ponds that we will be studying succession on.

Right now they (the people who set up and monitor the tanks) are rinsing the containers with freshwater as well as rinsing the sand with freshwater. The sand is going into the containers as they are getting rinsed. We will take a few samples here before anything else gets added.

Then they will fill the containers with new saltwater and run pumps for a few days with just the new seawater and sand. (too make sure everything is working well) This should be done by mid December. We will also take a few samples here.

Still in mid December (hopefully) they will  add old sand, rocks and animals from old reef tank.  This is where we will start extensively taking samples because we really want to see how the microbial communities become established. We will sample lots for the first couple days and slowly decrease the amount of sampling for the following few weeks. This is because we know most of the changes will happen within the first couple of days.
Then they are going to add live rock that have been curing. Curing basically gets rid of the dead stuff so the live and healthy organisms can thrive! We will again sample more extensively immediately after the rocks are added to catch the rapid changes happening to the microbial communities. We also might sample the rocks before they are put into the ponds.
After a short adjustment period due to all the new organisms, they will begin to populate the ponds with corals and other inverts. Once again we plan to sample a lot for the first few days but continue to sample, but less often after the first few days.

The next change that we predict will occur when students begin to reach into the ponds in the Spring. We will sample during this time too, to see how human interaction affects the microbial communities.

 

That’s the plan for now! 🙂