Correcting for rRNA copy # in qPCR experiments

Asked this question on Twitter and thought I would share answers here via Storify.  I am putting it below the fold to allow people to avoid the Storify embed if they want to.

From iSEEM project: Phylogenetic Diversity Theory Sheds Light on the Structure of Microbial Communities

Quick post.  Another paper is out based on the Gordon and Betty Moore Foundation funded iSEEM project I co-ran with Jessica Green and Katie Pollard.

PLOS Computational Biology: Phylogenetic Diversity Theory Sheds Light on the Structure of Microbial Communities.

O'Dwyer JP, Kembel SW, Green JL (2012) Phylogenetic Diversity Theory Sheds Light on the Structure of Microbial Communities. PLoS Comput Biol 8(12): e1002832. doi:10.1371/journal.pcbi.1002832.

It has one of my favorite paper figures ever.

Figure 1. The local community and metacommunity framework casts local biodiversity of coexisting species in terms of a sampling process from a larger reference pool, or metacommunity. 

And the paper is definitely worth checking out.

Does phylogeny matter? (In Eco-Evo meta-analyses) ... Apparently, yes, but it depends.

As many may know - I am pretty obsessed with the uses of phylogeny in biological studies.  In fact, one could say this has driven almost all of my work.  Thus when an email went around a little bit ago about an article for a journal club at UC Davis where the title begins with "Does phylogeny matter?", well, I had to take a look.  Alas, I was a bit worried when I saw the article was in Ecology Letters because I am at home and was not sure about access policies for this journal.

But I was pleasantly surprised to get full access without any library - VPN login to the following article: Does phylogeny matter? Assessing the impact of phylogenetic information in ecological meta-analysis - Chamberlain - 2012 - Ecology Letters - Wiley Online Library.  I cannot figure out WHY it is freely available right now, nor how long it will be, but I took the chance to look the article over.

And I was even more pleasantly surprised to look over the article.  Many meta-analyses can seem forced - if not almost unbearable to look through.  But this one is very well done.  Basically they did a massive comparison of conclusions that one could reach when one either does or does not take into account the phylogenetic non-independence of taxa when conducting meta-analyses in evo-eco studies.  They searched published literature for meta-analyses and then .. well I will use their words here (from the end of their introduction):

Some answers to "Wanted-good simple guide to the statistics of sampling design for field ecology studies"

I asked a question on twitter "Wanted - good simple guide to the statistics of sampling design for field ecology studies" and got some useful answers, which I have "storified" below. Any additional suggestions welcome.

YHGTBFKM: Ecological Society of America letter regarding #OpenAccess is disturbing

Wow -- I am really disturbed by the letter the Ecological Society of America (ESA) has written to the White House OSTP in regard to Open Access publishing. (For some background see Dear Representatives Issa and Maloney - Are you kidding me? Stop this bill now #ClosedAccess and Calling on Publishers to Resign from The Association of American Publishers Re Anti-Open Access Stance).

In the letter they make many statements that bother me deeply including:

However, it is important to note that there is a significant difference between research results and peer-reviewed publications.

Really - how are they different exactly?

Publishers such as ESA have a long record of reporting, analyzing and interpreting federally funded research.

OMG - seriously?  Apparently ESA is doing the analyzing and reporting and interpreting.  Not the scientists writing the papers.  But the publisher.  Seriously.  This is completely ridiculous.

It is not appropriate for the federal government to expropriate the additional value publishers add to research results.

They can't be serious.  This is not expropriation in any way.  This is the trying to guarantee that research taxpayers have paid for - that is done by scientists that taxpayers pay the salaries of - is not then published in a way that forces the taxpayers to pay for it again.

Furthermore, subscription revenue helps to support other Society services, including scientific conferences, education programs, and the distribution of science information resources to policymakers and the public.

So now what they are saying is that the government should hand them money via subscription fees so that they can then carry out some services they think are important.  How about this - how about the ESA applies for peer reviewed grants to fund their activities so that these can be reviewed by others.  As it is ESA can do whatever it wants with that money - being fed to it without any peer review - via indirect costs and grant money.

Papers published in ESA journals may therefore be just as relevant in several years as they are today, which means that any potential embargo period will do little to mitigate the financial losses that would result from full open access.

So - the justification here for not making ecological articles available is that they are MORE important over time?  So the taxpayers pays for research that is valuable and because it is valuable over time we should make it less freely available?  Seriously?

And here is the best one:

One way to make taxpayer funded research more visible and accessible to interested members of the public would be to require federally-funded grantees to provide a second version of the research summaries they already prepare, specifically for the lay reader. To aid in online searches, these summaries could also include the source of federal funding institutions and grant numbers. Publishers could also include grant information in paper abstracts which are usually available without a subscription.

That is right, they are suggesting that scientists write a second paper to go with their science papers that would be for the lay reader.  And that these summaries could include grant IDs to help in online searches.  WTF?  So now rather than making the actual scientific papers available they are proposing that scientists write a second paper because lay people would not be able to understand the first paper?  And what about scientists who want to read the papers but are at small institutions?  And never mind that "open access" is not just about money - it is also about "freedom" in the usage of published material.

The ESA has really gone off the deep end on this.  I note - I am in full support of companies and publishers making money.  I am also generally against government regulations.  But this issue is about taxpayers rights, government waste, and the progress of science.  It is simply inexcusable for the government to not use taxpayer money judiciously.


If the government pays for the research, pays for the research supplies, pays the salaries of researchers and peer reviewers, then it is unacceptable that publishers would then limit access to papers and force taxpayers to pay for them again.

The ESA basically is saying "taxpayers should be required to subsidize us".

Or - another way to look at this - ESA is saying: "Taxpayers - we want your money -but you are too stupid to understand what we are doing with it."

Ridiculous.

Hat tip to Karen Cranston for pointing this out.

Some responses to this post:

@phylogenomics Ecologists against public access to peer reviewed publications johnhawks.net/node/28402 <-- Not ecologists; lobbyists.
— Mike Taylor (@SauropodMike) January 7, 2012

@phylogenomics ESA seems to mimic AAA arguments against #openAccess from 5 years ago alexandriaarchive.org/blog/?p=840#ES…
— Eric Kansa (@ekansa) January 7, 2012

YHGTBFKM: Ecological Society of America letter regarding #OpenAccess is disturbing - bit.ly/AAfbEj disgusting/insulting, more like
— Glyn Moody (@glynmoody) January 7, 2012

RT @drcraigmc: Really shocked by this: Ecological Society of America letter regarding #OpenAccess is disturbing shar.es/WJuK3
— Carly Strasser (@carlystrasser) January 7, 2012

Yes, disturbing, to say the least! YHGTBFKM: Ecological Society of America letter regarding #OpenAccess is disturbing shar.es/WJkdI
— Madhusudan Katti (@leafwarbler) January 7, 2012

@carlystrasser @drcraigmc That is bad. I hate in when professional societies put their revenue models ahead of their members interests.
— Eric Kansa (@ekansa) January 7, 2012

Wow, scientists being downright merchant bankers about their revenue streams & tax-funded research: phylogenomics.blogspot.com/2012/01/yhgtbf… via @mattblaze
— Lee Alley (@lee_alley) January 7, 2012

"We want your money, but you're too stupid to understand what we're doing with it." phylogenomics.blogspot.com/2012/01/yhgtbf… #openaccess
— Michael Ekstrand (@elehack) January 7, 2012

#OA without programmatic access? So wrong. Publishers, make money while *making your product useful*, would you? bit.ly/AsHetK
— Heather Piwowar (@researchremix) January 7, 2012

Academics against open access: bit.ly/Albjqt. And a response: bit.ly/wa7tiP
— Kenan Malik (@kenanmalik) January 7, 2012

Why doesn't the Ecological Society of America allow their Open Access content to be text mined? wp.me/p22qQ8-22 via @wordpressdotcom
— Scott Chamberlain (@recology_) January 7, 2012

Still think science and politics don't mix?... fb.me/W58YnJVK
— Dr. Kiki Sanford (@drkiki) January 6, 2012

Open Access and Ecologists

Draft blog post cleanup #2: Metagenomics meets animals

OK - I am cleaning out my draft blog post list.  I start many posts and don't finish them and then they sit in the draft section of blogger.  Well, I am going to try to clean some of that up by writing some mini posts.  Here is #2:

Saw an interesting story on Genome Web: 'Denizens' of the Deep | The Daily Scan | GenomeWeb.  I have not been able to get the original article yet, but it seems that what they have done can basically be considered metagenomics for animals.  They collected sloughed off cells and other material from a lake and surveyed it for animal DNA.  This seems like a very cool derivative of metagenomic approaches and has enormous potential.  But alas, I never got down to getting access to the paper: Monitoring endangered freshwater biodiversity using environmental DNA so this will have to stay as a mini post.  Damn non open access journals ...

Tom Bruns talk on fungal dispersal at #UCDavis 11/10/11 #ecology #fungi

Quick blog post: interesting piece on the evolution of ecology by Simon Levin

There is a very interesting piece in the Chronicle of Higher Education by Simon Levin on the "Evolution of Ecology."

See The Evolution of Ecology - The Chronicle Review - The Chronicle of Higher Education

In it Simon, who I consider both a friend and colleague and who has been an inspiration to me for much of my work, discusses the history of the concept and the field of ecology. He repeats a key phrase he has used elsewhere:

Ecology, the unifying science in integrating knowledge of life on our planet, has become the essential science in learning how to preserve it.

I like this phrase and plan to use it a bit here and there, with attribution of course.

Levin also discusses how Darwin's Voyage of the Beagle helped launch the field of ecology because it

defined a new and synthetic way of looking at nature—in which the patterns characteristic of particular regions found explanation in a unifying, dynamic framework

It was only after Voyage of the Beagle and Wallace's work and others that the term "oekologie" came into being.

I particularly like the end where he connects ecology to study of other complex adaptive systems like economic ones and medical ones.

The article is really really really worth a read.

NSF looking for grants on "Life in Transition" re:climate change

Just got this email from the National Science Foundation saying that NSF is looking for more grants relating to responses of organisms/ecosystems to climate change.

The Divisions of Integrative Organismal Systems (IOS) and Molecular and Cellular Biosciences (MCB) in the Directorate for Biological Sciences at NSF encourage submission of proposals that address the biochemical, molecular, cellular, genetic and/or organismal underpinnings of adaptation and biological feedbacks to climate change.  Interdisciplinary and systems level approaches to these problems are encouraged. A cross-divisional working group has been established to ensure that exciting proposals in this area receive adequate and appropriate attention. 

Life on earth contributes actively to the forces involved in troposphere climate and chemistry. Not only are organisms key participants in climate and chemistry forcing functions, they are also highly sensitive to changes in many climatic and chemical properties of the troposphere.  Research is needed to understand the limits of biological adjustments to such changes, and the feedbacks on climate and chemistry that will result. 

The Foundation has a rapidly growing commitment to research directed towards understanding the interplay between living organisms and the earth’s climate and surface chemistry.  In the Directorate for Biological Sciences, this was emphasized last year by the establishment of a special Life in Transition activity, as announced in an open letter to the research community, accessible at: http://www.nsf.gov/pubs/2008/nsf08078/nsf08078.jsp?org=NSF.

Please consider submitting proposals of this kind to IOS and MCB using the ‘LiT:’ title preface described in the Life in Transition ‘Dear Colleague’ letter referenced above.  A project summary and introduction that place the proposed  research in the context of global climate change will be most helpful in determining appropriate sources of funding within NSF. 

If you seek further information, queries sent to this return email address will be directed appropriately to insure a prompt reply.