09 February 2016

Tuesday Crustie: Colour your own crustacean!


Colouring books for adults are popular now, so I applaud the BioDiversity Library for making this outreach tool! They have a whole big big available here.

Hat tip to Ely Wallis.

08 February 2016

The unenveloping* of Science Blogging!

It’s here!


It’s been a long time in writing and editorializing and proofing and printing (I first announced it in fall 2014), but the book is finally here! I can read Science Blogging: The Essential Guide! And you can’t yet, nyah nyah nyah!

Honestly, I’m excited not only as one of the chapter authors (first publication of 2016, I get to have some Canadian chocolate today!), but as a reader. I certainly didn’t know the complete list of chapter authors when I started writing. Looking at the other contributors to this volume is, frankly, terrifying. They are such great writers. I feel like:


I started working on my chapter on the plane to Science Online 2013. It’s almost exactly three years ago. I got 422 words written (less than many of my blog posts), which are still on my iPad. Here’s a snippet of the very start of the very first draft:

Ronin blogging
I have three science related blogs. I started what became NeuroDojo in 2002, followed by Marmorkrebs in 2007 and Better Posters in 2008,

There are advantages to belonging to a network, but they may not be as great as you think. Being on a network in and of itself does not guarantee readership.

While you are an independent blogger, you still need to develop a community.

And it goes on from there. Looking back at that first draft, it’s interesting to see how many of those first sketchy ideas survived into the final chapter.

I do have one disappointment in my chapter, though. Because this chapter references “ronin” as a metaphor extensively, I had wanted to pay tribute to Legend of the Five Rings and use this John Wick quote from one of the very first L5R promo cards, Dairya, to open the chapter:

“You call me a masterless man. You are wrong. I am my own master.”

Alas, that lead-in quote did not survive the edit, but I was able to get some L5R references in the main body of the text.

And the references to me being at The University of Texas-Pan American are also obviously out of date.

But I am so happy that this book is now out! I’m very happy with some of the turns of phrase in m contribution, and I cannot wait to work through everyone else’s chapters.

And, for the first time, something about this book has moved faster than expected! Previously, I announced it would be out 22 March, but Amazon is now showing it for sale on 1 March!

* Normally, the reveal of a fresh new something is called “unboxing,” but since this didn’t come in a box...

Bird picture from here.


External links

Science Blogging on Yale University Press
Science Blogging page of Facebook
Science Blogging on Amazon

Related posts

Incoming: The Complete Guide to Science Blogging
Incoming: Science Blogging
Science blogging book: now with blurbs!
Science Blogging: The Essential Guide book cover reveal

03 February 2016

Setting an agenda

Despite the title, committee chairs don’t have all that much power, particularly in academia. The whole point of having committees is that committees vote, and responsibility is diffused.

Committee chairs do have one actual power: to set an agenda.

I’m only a few days into my term as chair of the Student and Post-doc affairs committee at SICB, but I just want it to be known publicly that preventing sexual harassment of students and trainees has jumped to the top of the agenda.

This went to the top this morning when I opened my Twitter feed and saw, over and over, people discussing this article in the New York Times about an individual who harassed students at multiple institutions. This comes on the heels of other examples in recent months. This blog post could easily turn into a litany of harassment, so let’s just say this: there’s too much of that crap going on.

I don’t know whether harassment has been a topic of conversation for the committee before, but I look forward to finding out. If it hasn’t, it’ll be new. If it has, I plan to keep it front and center.

And I’m blogging this because I want to be accountable. I want people to know that this is what I want to try to do, so they can see if I succeed or not.

Related posts

Okay, SICB students and post-docs, I’m your guy

External links

Chicago professor resigns amid sexual misconduct investigation
Here’s how Geoff Marcy’s sexual harassment went on for decades
Work in progress: changing academic culture
You are worthy.

Photo by A Syn on Flickr; used under a Creative Commons license

02 February 2016

Who is Jingmai O’Connor, and why is she saying nasty things about science blogggers?

We’re less than two months away from an entire book about science blogging dropping from a major university press (disclaimer: which I have a chapter in), and here we have a reminder that many believe blogs are not a legitimate form of academic writing:

What’s your view on social media and science? For example, the role of science blogs in critiquing published papers? Those who can, publish. Those who can’t, blog. I understand that blogs can be useful in affording the general public insights into current science, but it often seems those who criticize or spend large amounts of time blogging are also those who don’t generate much publications themselves. If there were any valid criticisms to be made, the correct venue for these comments would be in a similar, peer-reviewed and citable published form. The internet is unchecked and the public often forgets that. They forget or are unaware that a published paper passed rigorous review by experts, which carries more validity than the opinion of some disgruntled scientist or amateur on the internet. Thus, I find that criticism in social media is damaging to science, as it is to most aspects of our culture.

This quote is from an interview with Jingmai O’Connor, a paleontologist currently in China.

Let’s break down the problems here.

Those who can, publish. Those who can’t, blog.” There are many researchers who do both, productively.

I understand that blogs can be useful in affording the general public insights into current science...” It’s nice that we bloggers got tossed a bone (no pun intended). But science blogs do not just help the general public; there are many technical comments on papers that help provide needed context for other scientists, whose own research is tangential to published research: close enough to see the relevance, but without the deep expertise needed to pick out specific problems.

(I)t often seems those who criticize or spend large amounts of time blogging are also those who don’t generate much publications themselves.” O’Connor is hypothesizing that there is an inverse correlation between blogging and primary literature. This an interesting empirical question. It’s true that time spent blogging is time that cannot be spent writing primary peer-reviewed journal articles, so prima facie, there might be truth to this. But as far as I know, there is no actual peer-reviewed literature on this. Will update this post if I find any.

If there were any valid criticisms to be made, the correct venue for these comments would be in a similar, peer-reviewed and citable published form.” The venue a claim is published in does not determine the validity of the claims. She is correct that certain journals are averse to citing non-peer reviewed material, and that putting material in the literature helps to assure the long-term findability of the critique. But these matters are not central to the main issue: is the criticism valid? Then it does not matter where it was published.

The internet is unchecked and the public often forgets that. They forget or are unaware that a published paper passed rigorous review by experts, which carries more validity than the opinion of some disgruntled scientist or amateur on the internet.” Some things on the Internet are unchecked. Some things on the Internet are rigoruously checked. It should also be noted that some journals that call themselves peer reviewed provide checks that are, at best, cursory (see here and here, for instance). Even “top” journals have published papers that made pro scientists ask, “How did this get published?” Has Dr. O’Connor not heard of arsenic life or STAP cells?

I find that criticism in social media is damaging to science, as it is to most aspects of our culture.” I’ve written a whole article (Faulkes 2014) about why I find that criticism in social media generally valuable. To name just two: it is rapid, and provides a way to bypass powerful gatekeepers with vested interests.

I have no idea what damaging effects of social media on culture she is referring to. It’s off topic, in any case.

Not surprisingly, as soon as someone on social media found this, this quote began spreading like wildfire. But there is apparently a backstory that is not spreading as fast. Jon Tennant wrote:

In this situation, she’s actually right. There's a core of semi-pro bloggers who attack her work/never formally publish anything.

I went digging. And I was surprised, because my first impressions are that Dr. O’Connor is not a stereotypical stick in the mud, conservative older scientist that is sort of the stereotype for critiques of blogging and social media. Honestly, she seems... kind of... awesome.

I went through the first ten pages of Google results, and found tons of positive stuff about her, including tons of stuff on blogs. She’s had lots of high profile papers. She’s done some science outreach. She strikes me as smart, outspoken, and a little unconventional. Jingmai O’Connor seems like exactly the sort of person I’d use a counter-example to the “scientists are old white dudes” stereotype.

I did a Google search for her name plus “blog.” Went through multiple pages and still found nothing negative about her, or controversies around her work. Tried her name plus “controversy.” Still nothing.

Maybe the blogging criticism is behind the Great Firewall of China.

Even when intentionally looking for the backstory that might have motivated her comment, I can’t find it. Whoever the bloggers are who have criticized her, they didn’t appear to make a big dent in her online reputation to an outsider like me. Which makes me all the more puzzled why she would paint all bloggers with such a broad brush.

It’s unfortunate. I hope that the criticism of her ill-advised comments don’t cement her “The Internet is bad” opinions. If she had a blog, I would be reading it.

Additional: Lengthened the blog post with a line by line fisking of the quote.

References

Faulkes Z. 2014. The vacuum shouts back: post-publication peer-review on social media. Neuron 82(2): 258-260. http://dx.doi.org/10.1016/j.neuron.2014.03.032

O’Connor J. 2016. Jingmai O’Connor. Current Biology 26(1): R11–R12. http://dx.doi.org/10.1016/j.cub.2015.11.046

External links

Jingmai O’Connor home page
Interview with Dr. O’Connor
A teacher can never tell where his influence stops
Fashionista: Jurassic Jingmai
Jingmai Kathleen O'Connor: Badass archeologist (sic)
Society for Vertebrate Paleontology 2014

Blogging is wonderful for science. More scientists should blog and tweet.
Chill out about Jingmai O’Connor’s criticism of bloggers

01 February 2016

DoctorZen.net moved


My home page, DoctorZen.net, has migrated over to a new institutional server. The old site will be up for a while until I get a redirect notice up, but it will eventually close as website support for my previous institution (The University of Texas-Pan American) transitions to my new one (The University of Texas Rio Grande Valley).

If you visit the site by a directly typing in the URL into a browser, you should see no difference.

If you bookmarked the homepage, take a moment to check that it links to the new URL:
http://faculty.utrgv.edu/zen.faulkes

You can let me know if there are any problems by emailing me at zen.faulkes@utrgv.edu.

Okay, SICB students and post-docs, I’m your guy

I knew this was coming, but I just got the official email.

I am writing to appoint you as Chair of the Student & Postdoctoral Affairs Committee within the Society for Integrative and Comparative Biology. Your appointment will be for three years, starting immediately and running until the end of the annual meeting in January of 2019.

I had been approached about this back before the last SICB meeting in Portland. I thought a very, very long time before stepping up and accepting this.

I was extremely hesitant about being another old white guy in a leadership position of a scientific society. This is especially true of a leadership position that is about engagement of young researchers, the place where our diversity in the sciences is the greatest.

I also paused when I considered that I’m at an institution with no doctoral programs or post-docs. Yes, I’m a graduate program coordinator for my department, but it’s a master’s program. Would I be in touch enough with the realities of the more advanced training programs that would make up the bulk of the constituents?

Finally, I had a truly selfish reason: committee work will cut into research time. And the research had been going well, and I don’t want that to stop.

Ultimately, one of the main reasons I agreed to do this was that the hint was dropped that if I didn’t do the student committee, the Executive Committee would keep after me to do something for the society. The judgement had been rendered, and it was all a question of how sentence would be carried out. I picked the devil I knew versus the one I didn’t.

29 January 2016

Rabid Alaskan foxes



Karsten Hueffer was on our campus yesterday, giving an interesting talk on the biology of rabies in Alaska. And yes, whenever someone from Alaska comes to Teas, there were a few pointed jokes about the relative size of the two states.

Rabies is one of those diseases that almost everybody knows about, but not very many people actually experience it, either directly or indirectly. (Well, in North America, anyway: about 50,000 people worldwide die of rabies annually.) The pathology of rabies is still not understood: the brains of people who die from rabies are not dramatically different from those of people who don’t have rabies. almost 100% mortality for people who are infected.


Rabies in Alaska is a big problem, and is primarily spread by foxes. Most cases of rabies occur along the Alaskan coast, where arctic foxes predominate. Red fox dominate central Alaska. Hueffer hypothesized that Arctic foxes are main rabies reservoir, and red foxes are just spillover hosts. He tested this by examining the three different strains of rabies, and looking at the population structure of the arctic foxes. It turned out there were three populations of Arctic foxes, and they all lined up very well with the three rabies strains.

Hueffer went on to do some species distribution models of rabies, to answer why is there no significant rabies problems in central Alaska? The models predicted rabies distribution well, but was also good at predicting the occasional outbreaks that occur sporadically in central Alaska. The species distribution models also predicted that the rabies will retract in the future, due to climate change.

Hueffer then switched gears to look at how rabies affects its host mammals. Normally, lethal infections doesn’t spread well, because the hosts are killed before the infection spreads. Rabies is able to beat this problem, in part, by manipulating their hosts into biting other animals. One protein in the rabies virus binds to nicotonic acetylcholine receptors, which are surprisingly similar to snake bungarotoxins.

In collaboration with molecular biologists, Hueffer and colleagues were able to create a toxin that was derived from the rabies protein (basically, a portion of the whole protein, if I understood right). From an experimental point of view, this is convenient because you can study the effects of rabies on nervous systems with none of the normal immune responses, and so on, that are triggered by infections.

They were able to show in a disk that this toxin interacted with acetycholine receptors. They then moved to testing their toxin in Caenorhabditis elegans (a.k.a. “a worm model”), and the rabies-derived peptide blocked normal feeding in their worms.

When this rabies-derived peptide was put in mice, the effect on behaviour was dramatic. The infected mouse kept running around its cage, up to ten times more than control mice. This strongly suggests that the virus is manipulating its host by directly interacting with neuronal receptors. While many viruses bind to cell receptors, usually they are doing do to trick the cell into bringing the some part of the virus into the cell. Rabies does not get into the neurons at all.

The entire rabies virus consists of just five genes. Rabies appear to be a particularly nice, simple model for behavioral manipulation by infectious agents.

External links

Karsten Hueffer’s faculty page
Karsten Hueffer on Google Scholar

Fox photo by Ralf Κλενγελ on Flickr; used under a Creative Commons license.

28 January 2016

The cost of selectivity


Scientific Reports and Nature Communications are both published by the same company, Nature Publishing Group. Both are online only, open access journals.

But Eigenfactor pointed out that Scientific Reports charges an article processing fee of US$1,495, while Nature Communications costs more than double that, US$5,200.

Why the price difference? Since they are both at the same publisher, it’s obviously not a simple infrastructure difference, like one journal having a physical print run, different manuscript submission systems, and so on. Both appear to offer the same services to authors.

There seem to be two factors that might explain the price difference: staff and selectivity.

Scientific Reports seems to be run by editors who are working scientists. Presumably they are not drawing most of their salary from the publisher, and are working mostly on a volunteer basis, which is common for scientific journals. The editors of Nature Communications are Nature Publishing Group staffers, who presumably are getting salary from the publisher. I wonder what the expected and actual difference in outcomes are between these two editorial schemes.

Neither journal seems to report what percent of manuscripts are ultimately published, but the criteria for Scientific Reports is that research be “scientifically valid and technically sound.” On the other hand, Nature Communications says it publishes “important advances of significance to specialists,” so clearly it is setting itself up as the more exclusive club.

Why be selective in a purely online journal? There is no limit to the number of pages, and I expect the cost of server storage per paper is fairly trivial. The selectivity is no doubt to increase journal Impact Factor, which in turn drives prestige and desirability. And at first glance, it seems to be working: the journals’ web pages report Scientific Reports Impact Factor is about 5, and Nature Communications is 11 and change.


But... the blog for Frontiers in journals (owned by Nature, incidentally) has a post claiming there is no relationship between Impact Factor and rejection rates. The problem that James Hardcastle and Anna Sharman pointed out is that while they archived data on Figshare, the data does no include journal names, so it’s not verifiable.

As far as I can tell, the only revenue stream for these journals is their article processing charges. As I mentioned before, this means that published papers are subsidizing the costs for the rejected ones. When I started this post, I though the comparison of these two journals might give a glimpse into just how big that subsidy is. But it’s hard to disentangle from the differences in editorial management.


I’m intrigued by all this because the open access “baby journals” that share the name of a paywalled glamour magazine (Science, Nature, Cell) seem to be able to charge prices that are well above the market for most open access journals. Te reuse yesterday’s graph, they all break the axis:


I’m curious as to why this pricing scheme survives. Do people confuse Nature Communications with Nature? Is the reputation of the publisher just that strong that it commands a premium, even for a relatively new journal? Is there no competition on value or services to the authors? Do people really expect ten times the prestige because they paid ten times the cost?

Related posts

Fluctuating publication costs

External links

Selecting for impact: new data debunks old beliefs

“And by the way... this is called gravity.”

Neil DeGrasse Tyson was uncharacteristically scrappy on last night’s episode of The Nightly Show, taking on B.o.B. over the flat Earth idea. I love it.



In a free society, you can and should think whatever you want. You want to think the world is flat, go right ahead. But if you think the world is flat and you have influence over others, as would successful rappers or even presidential candidates, then being wrong becomes being harmful to the health, the wealth and the security of our citizenry. Discovery and exploration got us out of the caves. And each generation benefits from what previous generations have learned. Isaac Newton, my man, said, “I have… If I have seen farther than others, it’s by standing on the shoulders of giants.” Can I get an amen?! So that’s right, B.o.B. When you stand on the shoulders of those who came before, you might just see far enough to realize the Earth isn’t fucking flat.

And by the way… This is called gravity. [mic drop]


External link

The Nightly Show video