Herd Immunity

vaccination

Over the past several years there has been a growing trend of parents that are terrified of vaccinating their kids citing reasons such as the debunked link to autism or that it just isn’t “natural.”   A healthcare blog run by several infectious disease doctors called Controversies in Hospital Infection Prevention has run frequent stories reporting on the declining vaccination rates as well as problems that ensue because of that, most recently about the whooping cough epidemic in Washington and wondering why Jenny McCarthy has so much influence on national views on vaccinations.

Continue reading

Advertisements

Averting the Approaching Apocalypse

This post is a guest contribution by Dr. Levi Morran, NIH postdoctoral fellow at Indiana University. Levi studies the role that both coevolutionary relationships and mating systems play in shaping evolutionary trajectories. His research using experimental coevolution to test the Red Queen hypothesis recently appeared in Science and was featured on NPR and the BBC.

electron micrograph of the aerobic soil bacterium Pseudomonas fluorescens(photo credit http://bacmap.wishartlab.com/organisms/500)

Electron micrograph of the aerobic soil bacterium Pseudomonas fluorescens
(credit BacMap)

I’ll begin by acknowledging that the title of this entry is probably a bit more dramatic than it needs to be. Nonetheless it’s pretty catchy isn’t it?

Given that the human population seems to have survived that whole 2012 Mayan calendar thing without incident, I know several of my friends (I won’t name names, but you know I love you) that would immediately think about zombies upon reading this title.  However, I am not particularly concerned about the extinction of the human race at the hands of zombies. For one thing, I need more evidence (or in fact any evidence whatsoever) before I buy the whole “zombies will rise up and end us all” fear. Further, Max Brooks (son of Mel Brooks) has given us a hilarious and potentially mildly effective guide to surviving the zombie apocalypse. Ultimately I am far more concerned about bacteria. To avoid inducing mass panic, I’m not talking about a terrified level of concern here, but certainly concerned enough to give it some thought.

Why bacteria? Well, the human population is currently in an evolutionary arms race with many of the bacterial species that infect us.  We continue to hurl scores of antibiotics at bacterial infections, imposing very strong natural selection, with little regard for the evolution of antibiotic resistance in those bacterial populations. Using current strategies in medicine, we are forced to administer greater doses of drugs or develop novel antibiotics to combat infections as the bacteria evolve greater levels of resistance (Levy and Marshall 2004, Martinez et al. 2007). This is a vicious cycle. I believe it is time to develop new strategies of managing our pathogens and treating infections. Thankfully there are many people that agree and are conducting ground-breaking research in this area, like Andrew Read’s group at Penn State University.

A paper by Quan-Guo Zhang and Angus Buckling (2012) takes an experimental evolution approach to begin addressing this issue empirically. In search of a different strategy for curbing the evolution of antibiotic resistance in their experimental populations of the bacterial species Pseudomons flourences, Zhang and Buckling treated their bacterial populations with either antibiotics, a bacteriophage or “phage” (a virus that attacks bacteria), or a combination of the antibiotic and phage. Zhang and Buckling predicted that the combination treatment might be more effective than either antibiotics or phage alone because the combination treatments should better reduce bacterial population sizes and limit their response to selection (Alisky et al. 1998, Chanishvili 2001, Comeau 2007). Additionally, bacterial mutations that confer resistance to antibiotics generally do not also confer resistance to phage, so evolution of resistance to the combination treatments would likely require at least two mutations, and thus require more time to evolve resistance than the other treatments (Chanishvili 2001, Kutateladze 2010). Continue reading

Predatory Open-Access Journals: Part 2

For much of the last week, I have been looking for a solid reason to either go ahead or not ahead with a manuscript I submitted to HOAJ Biology, a journal I later discovered made Beall’s List of Predatory Open-Access Publishers. There were many good reasons, in my mind, to just do it – it was peer-reviewed, my article and software are sound (though a minor contribution) and I would like closure on this project I finished a year ago. It turns out, there are some even better reasons not to publish with this journal. First and foremost, there is a FICTIONAL PERSON on the Editorial Board.

Shortly after this post, Dr. Todd Vision, with NESCent and UNC Chapel Hill, emailed me and asked if he might be of help. After sending him the manuscript with some additional details, he replied with this advice:

As for HOAJ Biology specifically, <an editor’s name deleted> may be legitimate, but that doesn’t mean he actually helps oversee peer review. I suggest you look up the credentials of another one of the editors, Peter Uhnemann, before you draw any conclusions about the involvement of the editorial board: http://phylogenomics.blogspot.ca/2012/01/scary-and-funny-functional-researcher.html

I highly recommend people read that whole post, but for those in a hurry: “Peter Uhnemann” from the “Daniel-Duesentrieb Institute” is a fictitious person from a fictitious institution. And he’s listed plain as day on HOAJ Biology’s Editorial Board! (I did contact one person on the Editorial Board via email to make sure he was actually affiliated with the journal, which he confirmed, but I guess that didn’t cut it.)

So, I am retracting my submission and going instead with either arXiv or figshare, which are non-peer reviewed, but citeable places to deposit research articles and/or software.

Dr. Vision also shared this advice with me for future manuscripts:

There are technical aids to finding the right journal in which to publish (like http://www.edanzediting.com/journal_advisor) but in the end one still needs to make a personal judgement about how to weight the many different factors. And while I am personally a strong advocate for gold OA journals, paying for publication upfront does require us as researchers to be more informed about the choices – library subscriptions no longer keep the low-quality publishers out of the market. In the future, if you are trying to decide among OA publishers, members in the OASPA (http://oaspa.org/membership/members/) is generally a reliable indicator of being on the up and up.

So what to do if you say no? If you aren’t interested in sending it to a more reputable outlet for minor contributions (like, say, BMC Research Notes), you could simply post it as a technical note on your website (a very common thing in CS) or on a preprint server like Figshare.

We’ll support you whatever you decide.

I am grateful to Dr. Vision (and Dr. Jonathan Eisen for the original post about “Peter Uhnemann”) and to all the commenters here for advising me when I really wasn’t sure what to do. (Final note: I suppose I should say that my experience with HOAJ Biology doesn’t mean all the smaller, open-access journals out there are Bad. Doing my homework paid off, though!)

Predatory Open-Access Journals?

Last summer, I worked with NESCent and Google’s Summer of Code to write a small piece of software. I think it’s quite useful for the specific thing it does and some researchers in my immediate peer group who have used it agree. I wrote up a short manuscript describing the program and very quickly got it rejected from Molecular Ecology Resources and Bioinformatics. It went on the back burner for several months until I got a solicitation from a new open-access journal that was offering a discounted rate for articles received before a certain date. So I submitted to this journal, after looking up some of their papers and a few people that have published there and convincing myself it wasn’t a flat-out scam.

One day after I submitted, I got an email asking me to review my own article. I know, right? How could that ever happen with a legitimate journal? I declined, they sent it to others to review and about a month later I got three reviews back that were short (0.5 – 1 page), but addressed real questions about my manuscript and included helpful suggestions. I incorporated the changes as best I could and resubmitted. About a week after the resubmission, I saw Beall’s List of Predatory Open-Access Publishers, which includes the aforementioned  journal on the list of “questionable, scholarly open-access publishers”. The author of the list says: I recommend that scholars not do any business with these publishers, including submitting articles, serving as editors or on editorial boards, or advertising with them. Also, articles published in these publishers’ journals should be given extra scrutiny in the process of evaluation for tenure and promotion.

Then, this morning, I got final acceptance of the manuscript and I’m not sure what to do.

I’m not trying to pull one over on anyone and I don’t necessarily disagree with the above text, but I don’t think this paper will be able to go anywhere else and I’m not convinced this journal is Bad. Not a lot of places publish small pieces of discipline-specific software (if you know of any, let me know). I believe this would be a really useful tool for some biologists and in fact, there are a couple of people waiting to cite the manuscript. I don’t want to encourage predatory journals, but open-access articles that do not-super-important science might actually have a place in our field.

I would LOVE thoughts on this. I certainly don’t view this manuscript as equivalent to a Molecular Ecology or Evolution publication – but do all pubs have to be top (or middle) tier? Is there a solution here, like including impact factors on CVs? Or maybe new fangled software like Google Citations can alleviate this problem since they show the overall publishing record of an individual/article? Please weigh in!

(PS – I’m not usually a fan of baby pictures, but come on. It’s a fat, funny baby. He looks like he’s made of marshmallows.)

(PPS – There’s a follow-up post here.)

Tell the White House: Make government-funded research open-access

As J.B.S. Haldane put it, “I think … that the public has a right to know what is going on inside the laboratories, for some of which it pays.” He was referring to the need for scientists to explain their work in popular media—which, amen, brother Jack!—but the point holds with regard to access to original scientific articles, too.

It doesn’t make much sense that U.S. citizens, whose taxes fund most of the basic science in this country, are then expected to pay upwards of $50 for a single PDF copy of a journal article presenting government-funded research results. The National Institutes of Health already requires that research it funds be archived online and accessible to the general public free of charge—why not expand that to all government-funded research? And hey, there’s a way to suggest exactly that out to the man in charge: a petition on WhiteHouse.gov.

We believe in the power of the Internet to foster innovation, research, and education. Requiring the published results of taxpayer-funded research to be posted on the Internet in human and machine readable form would provide access to patients and caregivers, students and their teachers, researchers, entrepreneurs, and other taxpayers who paid for the research. Expanding access would speed the research process and increase the return on our investment in scientific research.

The highly successful Public Access Policy of the National Institutes of Health proves that this can be done without disrupting the research process, and we urge President Obama to act now to implement open access policies for all federal agencies that fund scientific research.

It needs 25,000 virtual signatures within 30 days before it’ll get any meaningful attention, so sign this thing and then start badgering all your online “friends” about it, why don’t you? Especially the jerks who keep filling your update stream with branded product promotions and/or time-sucking adorable cat videos and/or news about how they’ve just spent real money for a virtual cow—post this directly on their “walls,” if those are even still a thing, with or without a witty and/or pleading comment appended.

I mean, it’s Monday morning; it’s not like you’re going to get do anything else for the benefit of humanity in the next minute or two, you slacker.