Lousy attack on open journals just reveals poor peer review

Michael Eisen took a stab back at a news item in Science that attacks open access journals for accepting a fake paper that was deliberately flawed. The Science column has the heading:

A spoof paper concocted by Science reveals little or no scrutiny at many open-access journals.

Yet, that is not what the study can conclude. Any basic study needs a control, in this case it would have been traditional, subscription-based journals.

This study can only reach the conclusion that fake papers can make their way in open access journals, but not that it is a problem of open access journals, as some have said. A similar study in closed journals was needed to be able to say this. In fact, the premier publisher of open access journals, PLoS, rejected the paper.

As an example, Science was the journal that published the, now proved deeply flawed and wrong, arsenic life paper. That paper had so many flaws, several scientists had already made the questions editors and reviewers didn’t ask in just a couple of days, in particular Rosie Redfield. Science needs to get down their high horse and see the problem for what it is: people will do anything to publish anything, so predatory and lazy journals abound. Publication has taken precedence over the science.


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The frustrating case of chytridiomycosis researchers

I began my research career working with amphibians, in particular the Eleutherodactylus frogs of Puerto Rico. One of the reasons I distanced myself from the whole area, other than just finding new interests, was largely a feeling of frustration over the lazy science that was taking place and occupying all the spaces, and funding, in amphibian declines: chytridiomycosis. This disease is caused by the chytrid fungus Batrachochytrium dendrobatidis (Bd) and has been associated with population declines and extinctions in several places in the world since the 90s. The problem is that big conservation projects are being put in place while basic questions still get no attention.

Although Koch postulates were met (the disease is caused by the Bd and it can kill individuals after infection), there is more than plenty of evidence that some species and populations can survive or are not affected by Bd. Why most researchers in the area still talk about presence as reason enough for a threat to all the species in an area?

I attended the 2013 ESA meeting and one of the presentations was on a model of infection of the disease. The problem was that the model made several assumptions that were obviously wrong, but were not justified. In particular, the presence of the zoospores in the medium was ignored, when it is known that the fungus has to re-infect the individual from the outside. The fungus creates more zoospores in the skin cells, which are expelled to the medium to infect other cells. Cell to cell infection seems to not take place.

Another example of the many problems in this area is the case of the “wave” of infection of Bd that covered Central America. The problem with this wave was that the analysis ignored everything we know about landscape ecology, infectious diseases, and even the Bd fungus biology. This fungus, which travels only as a zoospore in water, supposedly crossed the whole of Central America, across mountains, cities, and vastly different landscapes, at a steady rate. No alternative hypotheses were tested or any known animal or human epidemic was used to justify the wave hypothesis.

In the case of Puerto Rico, Bd has no effect on the most common species, yet some researchers insist on studying it as a threat. Last I heard, the only way they found to infect and kill the frogs was submerging them in a solution with an insanely high density of the fungus, something that will never happen in the field. Again, biology and infectious disease behavior were ignored to sustain the story of a “risk” of Bd.

In the case of the presentation I saw at ESA, I asked if there had been any comparison with infectious disease models, data, or examples – the answer was “no”. How come there is so much money being invested into this problem, yet no one can tell if it behaves like any known disease, in order to learn more from it? How come zoos are going crazy building “amphibian arks” to save species without first confirming that Bd is a threat to the species they are removing from the field?


Posted in Declining Amphibian Populations, Meetings, Science | Leave a comment

First look at the new Cosmos 2014

“It is time to get going again.” – Neil deGrasse Tyson

In 1980  on one of the most important and influential science documentaries aired, Cosmos: A Personal Voyage, narrated by the incomparable Carl Sagan. In this documentary, of 13 chapters, Sagan made ​​a trip exploring about a variety of topics, including the history of science, cosmology, evolution, pseudoscience, Mars, the brain and to the responsibility we have as a society.

After a generation that did not know the unique style of Cosmos, the heir to the seat of Sagan, Neil deGrasse Tyson, brings the new version of Cosmos: A Spacetime Odyssey in 2014. Along with Ann Druyan (Sagan’s widow) and thanks to the influence of Seth MacFarlane (Family Guy), the documentary will be televised on Fox. A few days ago, this trailer gave us a first glimpse of what to expect:



Among other details, the new version will not assume that the viewer knows the original version, but will seek to reach the highest diversity and number of people. This accessibility and unique style allowed the original Cosmos to impact more people than any other series has. The new series does not seek to copy the original, but to use the elements that touched people the most to tell the most important story today: what we know about our universe and how we know it.

For those interested, the original version of Cosmos is available on Netflix.


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Listening for species

The good friends, and mentors, of the Automated Remote Biodiversity Monitoring Network (ARBIMON) got a lot of press this week after a new publication in PeerJ. They have developed a system that researchers can train to detect species calls automatically. More importantly, they tested their system with data from tropical forests, which present a particular challenge due to the high biodiversity.

Some of the media outlets that covered their research:


Posted in Bioacoustics, Puerto Rico, Science, Sensors, Tropical Ecology | Leave a comment

I wanna be like Neil, or why I was crazy enough to get into grad school

When I grow up (in my career), I wanna be like Neil.

Not Neil Patrick Harris, the talented actor and star of How I Met Your Mother and Doctor Horrible’s Sing Along Blog. The other famous Neil:



Jump to minute 1:04 for a demonstration of his contagious passion with which he talks about science.

Neil deGrasse Tyson, the astrophysicist, science communicator, author, director of the Hayden Planetarium of the American Museum of Natural History in NYC, god to Stephen Colbert, and (in the only justified use of Auto-Tune) featured star in the Symphony of Science:



During the last couple of weeks I’ve been meditating a lot and looking to recover the inspiration that led me to take the crazy plunge into grad school. This can be a draining experience and I’m still getting out of the valley of shit. I’m out, but still trying to get rid of some bad habits. There comes a moment you can feel lost, then combine that with the moment when you like your project the least, family (thousands of miles away) problems, medical issues (and the bills that come with them), a bad case of impostor syndrome, living in a conservative Midwest town as a liberal and atheist Latino, and other personal issues. But at least the end is in sight, just have to jump the annoying hoops the grad school makes you jump. Continue reading

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A weak defense of the anti-GMO pig study

On recent days I got into an online discussion with an anti-GMO activist about the recent pig study that supposedly found that genetically modified soy and corn had a negative effect:

Judy A. Carman, Howard R. Vlieger, Larry J. Ver Steeg, Verlyn E. Sneller, Garth W. Robinson, Catherine A. Clinch-Jones, Julie I. Haynes, & John W. Edwards. 2013. A Long-term Toxicology Study On Pigs Fed A Combined Genetically Modified (gm) Soy And Gm Maize Diet. Journal of Organic Systems 8: 38-54. (AbstractPDF)

Many have destroyed their arguments (for example here, here, and here). The activist that I got into a discussion with, sent a long email with the replies from the principal author and some supporting press articles. I replied because it showed that there are in fact many problems with the paper.

Below, I copy the full replies to the criticism that I answered, with my comments in bold. You can see the full Carman’s posts at the website http://gmojudycarman.org



Prominent pro-GM activist, Mark Lynas has, as expected, attacked the study by Dr Judy Carman and her colleagues for their recent work titled, ?A long-term toxicology study on pigs fed a combined genetically modified (GM) soy and GM maize diet.?

Source: marklynas.org

ML: The authors are GM activists/campaigners and their results shouldn?t be trusted.

Answer Summary: The authors are not GM activists; they are highly credentialed experts.

Detailed Answer: Two authors are Associate Professors in Health and the Environment, School of the Environment, Flinders University in South Australia. Another is a Senior Lecturer at Adelaide University in South Australia. Two are veterinarians, one is a medical doctor, and two are farm experts. The authors have over 60 years of combined experience and expertise in medicine, animal husbandry, animal nutrition, animal health, veterinary science, biochemistry, toxicology, medical research, histology, risk assessment, epidemiology and statistics.

The principal author lists several publications that are anti-GM, including a chapter titled “Is GM food safe to eat?” at http://gmojudycarman.org/relevant-research/ The other qualifications are in no way denying the fact that Carman has published before against GM. This is a fact and should be considered as a possible bias or pet theory. This is not unique of this particular paper, but it is common occurrence in science. 

In addition, Carman lists on the website “Dr Carman’s government submissions” that are anti-GM (http://gmojudycarman.org/relevant-research/). That is an activist. Why deny that a scientist can be an activist too? There is nothing wrong with it, but the scientist has to be humble and consider a possible bias because her activism. Also, why deny it while accusing ML of being “pro-GM”?


Continue reading

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Nature Geoscience will test double-blind peer review

The journal Nature Geoscience has announced they will add double-blind peer review as an option for submitted manuscripts. They based their decision on a survey that showed majority support for this method and the strong possibility of bias against women in science.

This is great news, and I am amazed we still don’t have this option in all journals. I even think it should be mandatory, otherwise already established researchers will keep having an easier time than new researchers, instead of letting the best science talk by itself. Hopefully, the Nature name will provide enough influence for other journals to try this (ironic, I know), in particular if they get enough data to test the hypothesis that double-blind review removes biases.

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Mendeley sells out; I’m moving to Zotero

“The empire acquires the rebel alliance.” – a very common response in Twitter with the news of Elsevier buying Mendeley.

Yes, this is more on the side of poetic license than reality, but not by far. If you haven’t heard, Techcrunch reported last January on talks between Mendeley and Elsevier. Yesterday, it was confirmed that Elsevier bought Mendeley for an amount between $69-100 million. This announcement opened the floodgates of people denouncing the deal and Mendeley people’s promises that they won’t change. It was sad to see them try to promise something they will have no control over and never talking about any evidence or contractual obligations to protect what Mendeley is from what most people perceive Elsevier is.

Mendeley wasn’t an ideal solution. Mendeley Desktop is heavy and slow and their API was hardly documented. Mendeley admitted their public API is different from the API they used in their application and that the public API sucks. This deal now makes us question Mendeley’s commitment to open science.

This has nothing to do with dealing with for-profit companies or wanting everything for free. This has to do with a company that had become a parasite of research and that doesn’t deserve the benefit of the doubt, as Mendeley’s people seem to claim. They could have waited for Elsevier to show a true commitment to right their wrongs, but not, they want to become part of the rag Elsevier uses to try to clean up their image.

Elsevier has been denounced by editorial boards, libraries, thousands of researchers, and many other groups for their greedy behavior over content that is not generated by them. They bundle titles, forcing libraries to buy access to more than what they want. MIT has opted out of this at a premium. The company also was caught doing some shady business:

“[…] Elsevier put out a total of six publications between 2000 and 2005 that were sponsored by unnamed pharmaceutical companies and looked like peer reviewed medical journals, but did not disclose sponsorship, the company has admitted.” – The Scientist

Elsevier was among the companies that supported the draconian SOPA, until it became too hot to handle. As a reference, check the full MIT fact sheet on Elsevier. Basically, they oppose open access, squeeze the budget of libraries, and make an obscene profit from our work. A former developer, that moved to PeerJ, has written an interesting post on the matter.

Elsevier has also published some open access journals recently, that with the purchase of Mendeley, will be used to try to clean the company’s image. Their efforts for open science have been cosmetic. The question remains, what will happen when they change the current model of Mendeley service to universities to their hated bundles? What will happen when they close access to it to try to squeeze more money from us?

The satirical account @FakeElsevier just published this tweet that summarizes the discussions many have had with some Mendeley people during the last hours:


Moving from software to software

I’ve used several reference managers. The first was Endnote 3, but never had a big or important database since I had most of my references in paper. About 6 years ago I moved from Windows to Ubuntu and moved, as much as possible, to open source software. Endnote was not an option. Then, I started using Zotero when it was a Firefox plugin, but I found it limiting. I moved to Aigaion, a system based on Codeigniter that you ran in your own LAMP server. Unfortunately, Aigaion seems to have been abandoned, with their last release two and a half years ago, and their website is dead. I started to look for a new option. I think back then Zotero was available for Linux only as a plugin, so I went with Mendeley.


Time to move (hopefully for the last time) to Zotero

So, it was with great pleasure that i saw that Zotero now has a standalone application for my OS (Linux 64bit). They are also available for Windows and Mac and have plugins for Chrome, Firefox, Safari, and LibreOffice/OpenOffice. Moving from Mendeley to Zotero took some time, but reasonable for my large library, and it was easier than I thought. It will still require some cleanup and checking, but it is better than the alternative (staying with an Elsevier company).

I moved about 1600 references, with only around 50 without a file attached, with Mendeley Desktop version 1.8.4 and Zotero version 4.0.4 on Ubuntu 12.04 64-bit. The process should be the same in other platforms, but make a backup just in case. By default Zotero will upload your files to their servers. The free account is limited to 300MB, so if you have more than this, go to “Edit”, “Options”, then in the Sync tab unselect “Sync attachment files in My Library”.

I suggest working in batches if you have a large library. I worked 100 a time to keep it manageable.

  1. Create new folders in Mendeley. You will divide your full library into each folder.
  2. Select a bunch of references from your library and drag-and-drop to an empty folder.
  3. Delete those references from the main library (to avoid duplication). Once the drag-and-drop is done it is as easy as clicking Del on your keyboard.
  4. Go to the new folder, select all the references (Ctrl-A) and hit Ctrl-E.
  5. Save the references in RIS format.
  6. In Zotero, select “Import…” and look for the RIS file. If you have files attached, the RIS file should have the full path to the file in your disk and Zotero will copy it.

That is it. If Zotero works for you, support them by talking about it or getting a subscription. I’ll test it for a while and, if satisfied that it works for me, I’ll get into one of their plans: 2 GB for $20/yr, 6 GB for $60/yr, 10 GB for $100/yr, among other options. Worthwhile for our personal libraries.

If this helps or you find a problem, please feel free to drop a comment below.


Posted in Open Science, Papers, Science, Software | 11 Comments

The Nine Circles of Scientific Hell

A blog post by Neuroskeptic was so relevant that it got published in a journal! Neuroskeptic’s The 9 Circles of Scientific Hell got published in the November 2012 issue of Perspectives on Psychological Science:

Neuroskeptic. 2012. The Nine Circles of Scientific Hell. Perspectives on Psychological Science November 7: 643-644, doi:10.1177/1745691612459519. PDF

It is a funny but spot-on describing the sins of scientists. Check it out and avoid science hell.

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PLoS shows that publishing raw data can be a win-win situation

The PLoS blog Integrative Paleontologists has a cool story that shows why is it a good idea to have open data, or publish your raw research data. A paper in PLoS ONE studied dinosaur teeth, but what gave the authors the edge to answer the question they were after was being able to add data to their dataset from other papers. This allowed them to have a dataset of 1,200 data points!

A selection of carnivorous dinosaur teeth. These are representatives of eight tooth types that occur in rocks spanning 15 million years of evolutionary history–but the general forms surely represent more than eight biological species over this time! Figure 2 from Larson & Currie 2013.. CC-BY.

A selection of dinosaur teeth. Figure 2 from Larson & Currie 2013.

This is a win-win situation for everyone. Researchers Larson and Currie were able to merge the previously-published data with their own new data into a monster analysis (1,200+ data points, remember) that significantly advances science as a whole.

Why would we keep data we are done with when others can do more science with it?

Check out the post for the details.

Paper: Larson DW, Currie PJ. 2013. Multivariate analyses of small theropod dinosaur teeth and implications for paleoecological turnover through time. PLOS ONE 8(1): e54329. doi:10.1371/journal.pone.0054329

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