Comments for second half of January 2015

Small Pond Science has a look at science crowdfunding, which was partly informed by the PLOS ONE paper I contributed to on the subject.

The PLOS ONE paper also makes an appearance in a substantive article on science crowdfunding that appeared in several Australian newspapers, including The Age:

When crowdfunding sites first appeared about 2009, many scientists pooh-poohed the notion of raising research money through them, theorising that only those projects with gimmicky mass-market appeal – which they called “panda science” – would attract attention.

But that idea has been debunked.

In the first major study on crowdfunding in the sciences, which was published in December in PLoS One, the study's authors found that the online audience was willing to fund a wide variety of projects, even those in areas such as statistics or little-known invertebrates - which typically aren’t considered sexy.

What seemed to factor more in the success of a project was whether a researcher was able to develop a sufficient fan base. Being able to connect with a large audience through outlets such as Facebook, Twitter and YouTube appeared to correlate with increased levels of funding.

I’m a People of Canada!

I’ve taken over the @PeopleOfCanada Twitter account for the week!

I’ll be tweeting about maintaining a Canadian identity while living out of the country, a little science, and a maybe little more personal stuff than I normally get to at my usual Twitter account.

Join me for the week!

External links


Week 126: Expat Zen in Texas, USA

Maybe the UTRGV mascot should be the zombie, because the debate won’t die

Just when thought we had finished with the whole Vaqueros controversy, it’s back in the news. Texas lawmaker Terry Canales has made good on his threat.... er, promise... to introduce legislation that would almost certainly get rid of the “Vaquero” as mascot.

The bill, from my point of view, is... problematic. It reads:

The university shall include on the ballot:

1. the “Broncs”;
2. the “Ocelots”; and
3. any other options the university chooses, including nicknames nominated by students and approved by the university.

This is a rigged ballot for a single outcome: to get the Bronc back. It was clear in the discussion leading up to this that people affiliated with UTPA students favoured the Bronc, and everyone not affiliated with UTPA were “Anything but the Bronc.” Nobody was strongly arguing for the Ocelots.

There is no doubt that if there was a student vote held now, UTPA students would overwhelmingly vote for the Bronc.

I get that “majority rules” is very popular option... when you’re in the majority. It completely sucks to be given a message that what you have to say is not even worth listening to when you’re in the minority.

Let me give you a little “Zen predicts” on this bill: it will never come up for a vote, for two reasons.

First, legislators from the rest of the Texas will not see the value in interfering with a decision that was done above board and according to Hoyle. It was always Guy Bailey’s decision, and while his decision was unpopular, it was his to make.

Second, the UT System, and other Valley legislators from outside the Edinburg area, will lobby against this bill and stop it before it hits the legislative floor for a vote. The representatives of the UT System will resent what they see as political second-guessing and micromanagement. Other legislators will resent that the bill silences their constituents.

Additional, 27 January 2015: What also bugs me about the wording of this bill is that it removes the voice of any stakeholders other than current students. I’m faculty member, and I have a stake in this institution and am affected by mascot decisions (as much a students, at least). Why would I not get a say under HB901?

Maybe if the wording of the bill was “Vaqueros, yes or no?” I could get behind this bill, as it would address legitimate concerns about that particular mascot; that is, issues around cultural sensitivity, inclusion of men and women, and so on. But the point of this bill is to not to get passed. The point of this bill is for Representative Canales to be seen to be doing something.

External links

HB901
Bill seeks election for UT-RGV nickname
Proposed bill to leave UTRGV nickname up to students

A step back for UTRGV grad programs

Well, this is frustrating.

Currently, both The University of Texas-Pan American and University of Texas Brownsville handle graduate applications using a externally provided specialty system called Embark. Having used it for a few years, I can say it works well.

I learned yesterday that the new University of Texas Rio Grande Valley will use a completely new system for processing student applications to graduate programs. Actually, it’s already in place. It’s called ApplyTexas. It was intended to let students apply to any public university in Texas. Its sounds like a nice, simple idea: one system for students to deal with instead of many.

So, existing system that universities already have replaces subscription service, money saved, what’s the problem?

The problem is that ApplyTexas was designed to handle undergraduate admissions. It does not support attachments like personal statements or recommendation letters. To deal with this, it looks like applicants will have to go to ApplyTexas to enter their demographic data, then go to another website to upload documents, and then a third website to deal with recommendations. So instead of one common site, grad applicants will actually be interacting with three. The, they are “hoping” that all of the documents generated in these three systems can be combined into a single document.

And this decision was made after some UTRGV graduate programs had already started taking applicants.

It’s a mess.

Who decided this? The University of Texas System. Thanks a bunch, people.

Who paid for my open access articles?

A recurring concern from some researchers about open access is the cost to authors. This is an area of persistent misconceptions and a lot of fear. It’s a legitimate question of whether article processing charges create a Matthew effect, with labs with grants gaining an unfair advantage over those without grants. Or, worse, shutting out contributors entirely.

This interests me, because by most standards, I am a scientific “have not.” And yet, I’ve published many of my articles open access for some years now. I did not have stand alone research grants in that time. How did I do it?

It’s a mix.

The most common situation was that the journal did not levy an article processing charge. In other words, these papers were free to me. (In fairness, one – Aquatic Biosystems – was a limited time “free to publish” offer; they normally do charge a fee.)

• Jimenez SA, Faulkes Z. 2010. Establishment and care of a laboratory colony of parthenogenetic marbled crayfish, Marmorkrebs. Invertebrate Rearing 1(1): 10-18. http://inverts.info/content/establishment-and-care-laboratory-colony-parthenogenetic-marbled-crayfish-marmorkrebs
• Faulkes Z. 2011. Can brain imaging replace interrogation and torture? Global Virtue Ethics Review 6(2): 55-78. http://www.spaef.com/article.php?id=1266
• Faulkes Z, Feria TP, Muñoz J. 2012. Do Marmorkrebs, Procambarus fallax f. virginalis, threaten freshwater Japanese ecosystems? Aquatic Biosystems 8: 13. http://dx.doi.org/10.1186/2046-9063-8-13 *
• Faulkes Z. 2015. Marmorkrebs (Procambarus fallax f. virginalis) are the most popular crayfish in the North American pet trade. Knowledge and Management of Aquatic Ecosystems 416: 20. http://dx.doi.org/10.1051/kmae/2015016
• Faulkes Z. 2015. The global trade in crayfish as pets. Crustacean Research 44: 75-92. http://dx.doi.org/10.18353/crustacea.44.0_75
• Faulkes Z. 2018. Prohibiting pet crayfish does not consistently reduce their availability online. Nauplius 26: e2018023. http://dx.doi.org/10.1590/2358-2936e2018023

While I personally did not have grant support, our institution has had undergraduate training grants (notably HHMI). Those external grants picked up the tabs for a couple of papers with undergraduate co-authors:

• Puri S, Faulkes Z. 2010. Do decapod crustaceans have nociceptors for extreme pH? PLoS ONE 5(4): e10244. http://dx.doi.org/10.1371/journal.pone.0010244
• Joseph M, Faulkes Z. 2014. Nematodes infect, but do not manipulate digging by, sand crabs, Lepidopa benedicti. Integrative and Comparative Biology 54(2): 101-107. http://dx.doi.org/10.1093/icb/icu064

Lately, I’ve been fortunate to have my chair agree to support article processing charges of a couple of some papers from departmental funds.

• Carreon N, Faulkes Z. 2014. Position of larval tapeworms, Polypocephalus sp., in the ganglia of shrimp, Litopenaeus setiferus. Integrative and Comparative Biology 54(2): 143-148. http://dx.doi.org/10.1093/icb/icu043
• Faulkes Z. 2015. A bomb set to drop: parthenogenetic Marmorkrebs for sale in Ireland, a European location without non-indigenous crayfish. Management of Biological Invasions 6(1): 111-114. http://dx.doi.org/10.3391/mbi.2015.6.1.09
• Faulkes Z. 2018. Resolving authorship disputes by mediation and arbitration. Research Integrity and Peer Review 3: 12. https://doi.org/10.1186/s41073-018-0057-z

I paid the costs of a couple of few papers out of my own pocket. The two PeerJ papers were covered by a single lifetime membership, which was $99 at the time.

• Faulkes Z. 2010. The spread of the parthenogenetic marbled crayfish, Marmorkrebs (Procambarus sp.), in the North American pet trade. Aquatic Invasions 5(4): 447-450. http://dx.doi.org/10.3391/ai.2010.5.4.16
• Feria TP, Faulkes Z. 2011. Forecasting the distribution of Marmorkrebs, a parthenogenetic crayfish with high invasive potential, in Madagascar, Europe, and North America. Aquatic Invasions 6(1): 55-67. http://dx.doi.org/10.3391/ai.2011.6.1.07
• Faulkes Z. 2015. Motor neurons in the escape response circuit of white shrimp (Litopenaeus setiferus). PeerJ 3: e1112. http://dx.doi.org/10.7717/peerj.1112
• Faulkes Z. 2017. Filtering out parasites: Sand crabs (Lepidopa benedicti) are infected by more parasites than sympatric mole crabs (Emerita benedicti). PeerJ 5: e3852. https://doi.org/10.7717/peerj.3852

I paid the costs for two using indirect costs recovered from an external undergraduate training grant that I was awarded.

• Puri S, Faulkes Z. 2015. Can crayfish take the heat? Procambarus clarkii show nociceptive behaviour to high temperature stimuli, but not low temperature or chemical stimuli. Biology Open: in press. 4(4): 441-448. http://dx.doi.org/10.1242/bio.20149654
• Faulkes Z. 2017. The phenology of sand crabs, Lepidopa benedicti (Decapoda: Albuneidae). Journal of Coastal Research in press 33(5): 1095-1101. http://dx.doi.org/10.2112/JCOASTRES-D-16-00125.1

Update, 29 September 2019: One paper was paid for mostly by the indirect costs mentioned above, with my department kicking in the remainder.

• DeLeon H III, Garcia J Jr., Silva DC, Quintanilla O, Faulkes Z, Thomas JM III. Culturing embryonic cells from the parthenogenetic clonal marble crayfish Marmorkrebs Procambarus virginalis Lyko, 2017 (Decapoda: Astacidea: Cambaridae). Journal of Crustacean Biology: in press. https://doi.org/10.1093/jcbiol/ruz063

Finally, I don’t know how the article processing fee my most recent paper was the papers below were paid for by my co-authors.

• Byrnes JEK, Ranganathan J, Walker BLE, Faulkes Z. 2014. To crowdfund research, scientists must build an audience for their work. PLOS ONE 9(12): e110329. http://dx.doi.org/10.1371/journal.pone.0110329
• Patoka J, Magalhães ALB, Kouba A, Faulkes Z, Jerikho R, Vitule JRS. 2018. Invasive aquatic pets: Failed policies increase risks of harmful invasions. Biodiversity and Conservation 27(11): 3037-3046. https://doi.org/10.1007/s10531-018-1581-3

Looking at this list, I’m willing to bet that some researchers will say, “But Zen, even if you didn’t have traditional research grants to pick up the tab, you’ve still had a lot of support to pay for open access.” True. It’s hard to say if the number of open access papers would have been much different if, say, my department declined to pay for papers. I might have tried other journals, might have dipped into my pocket again, might have tried to find other pots of money.

From this perspective, the issue that might stop some researchers (retirees and amateurs, say) from publishing open access would not be “lack of grants,” but being disconnected from larger institutions. Being part of an institution brings a lot of infrastructure, and diverse resources that go way beyond who has external grants.

All of that said, several of my articles in “traditional” subscription-based journals also had page charges (one journal asked me for $320 for its 2.75 year publication process). It’s interesting to me that people don’t very often bring up those page charges as barriers to publication.

Additional, 17 March 2015: Updated list.

Additional, 2 August 2015: I added two new papers to the main list: one had no publication fees, the other was modest (PeerJ) and paid for out of pocket.

Additional, 18 November 2015: Added newest paper to list (reasonably low fees that I will pay for out of pocket).

Additional, 20 January 2016: Updated the list. One paper that I thought might cost me something ended up costing nothing. I also completed some citations.

Additional, 7 February 2017: Updated the list. Second time I dipped into some funds I have from indirect costs.

Additional, 10 June 2018: Updated the list, adding two more papers. And here’s a graph!

Additional, 18 June 2018: Updated the list, with one more paper. Graph above not updated yet.

Additional, 24 September 2018: While tweeting out this link again, I am reminded that I need to add Hilda Bastian’s important blog post about open access fees.

(N)ot having an APC doesn’t mean the journal is accessible to everybody. It has to accept work from your field. You have to be eligible to publish in it – an APC is not the only possible access issue. You have to write in its language of publication. And you want it to be accessible to people in your field. In mine, that means you really want it to be indexed in PubMed. And having DOIs is critical for citations to be counted by key systems.

Hilda does a little analysis to show that this winnows out to a small number of journals for most people.

Additional, 9 November 2018: Updated the list, with one more paper. Graph updated!

Additional, 29 September 2019: Updated the list, with one more paper.

Related posts

Waiving publication fees
The journal ecosystem

Photo by penguincakes on Flickr; used under a Creative Commons license.

Tuesday crustie: Buy garlic

“Those aren’t fangs...

“They’re claws!”

Geosesarma hagen is a new species dubbed a “vampire crab” in a new paper by Ng and colleagues (2015), and you can see why.

This interesting paper has details even more new and very colourful crab species. Another one is cream and bright violet. Several of these species were showing up in the pet trade well before this paper appeared, with completely unknown provenance. It’s a little scary to see how often collectors start pushing things into the pet trade even before we have a decent species description.

Another notable thing in the species names is that the crab Geosesarma dennerle, which the authors write:

The new species is named after the German company Dennerle, who kindly supported the third author’s study in Java.

It’s sort of weird, because first, it’s an aquarium company. This would seem to be a potential conflict of interest, which isn’t declared. Second, this funding source isn’t acknowledged anywhere in the acknowledgements at the end, which is the normal place you’d look for something like this.

Related posts

Tuesday crustie: I vant a cape!

Reference

Ng PKL, Schubart CD & Lukhaup C. 2015. New species of “vampire crabs” (Geosesarma De Man, 1892) from central Java, Indonesia, and the identity of Sesarma (Geosesarma) nodulifera De Man, 1892 (Crustacea, Brachyura, Thoracotremata, Sesarmidae). Raffles Bulletin of Zoology 63: 3-13. http://zoobank.org/urn:lsid:zoobank.org:pub:9F76CF88-A3DD-4F0E-B348-EEB9558DBBC4

Tuesday Crustie: Now, a little to the left...

I’m working up a storm to get a crayfish paper done before classes start next week, so I wanted to feature crayfish in this spot today. And I like this combination of critter and camera.

Photo by Steve Harwood on Flickr; used under a Creative Commons license.

New rule for medical research headlines

Dear science journalists—

I propose this simple rule for all headlines about medical research:

All headlines must include the species the research was carried out in.

I’ve suggested this a few times here and there on social media, but the latest case was the title of this Telegraph article:

Has Stanford University found a cure for Alzheimer’s disease?

My reaction might be summed up thus:

The problem is so obvious it doesn’t need a spoiler alert. The study was done in mice. Yeah. There have been a lot of studies on lab mice that suggested a cure for something or other was on the horizon. They often vanish without a trace.

Even after animal studies suggest that a treatment will be safe and effective, more than 80% of potential therapeutics fail when tested in people.

While “But if you read the rest of the article...” is a handy out for science writers, it doesn’t change that headlines are 90% of communication effort. If we’re going to improve science communication, headlines would be the place to start.

Imagine the difference in people’s response between the headline that was used and this:

Has Stanford University found a cure for Alzheimer’s disease in mice?

This provides people with a much more realistic idea of how far along the research is in that “bench to bedside” pathway.

External links

Betteridge’s Law

A cog in a teaching machine

In the Chronicle of Higher Education, Leonard Cassuto asked:

That phrase – “my own work” – has bugged me for my entire career. It’s always used to distinguish research from teaching, but how does teaching not qualify as “my own work”?

Teaching qualifies less as “my own work” because institutions clearly signal that I am a replaceable cog in their teaching mission.

Take introductory biology, for example. There are a bunch of textbooks out there. They all follow the same topics in the same order: Organic chemistry, macromolecules, cell structure, cellular respiration, photosynthesis, cell division, Mendelian genetics, DNA structure, replication, and protein synthesis.

My job in teaching is not to set the curriculum. Other people have done that. There is a very standardized introductory curriculum across North America, partly homogenized by the efforts of textbook publishers and the efforts of lawmakers. My job is to get up there and talk about the content that other people have decided I should teach.

Further, in my institution, there are multiple sections of introductory biology, each taught by different instructor. Since this is nominally the same class, the sections I teach must be broadly comparable in content, and to some degree delivery.

There are many lab sections, scheduled by a single lab coordinator, with topics selected to align with the expected lectures.

It should be no surprise that I don’t feel like teaching is “my” work, particularly at the introductory levels. I did not have much creative input into the content of the class, and I am very constrained in how I teach it.

If you want more evidence that institutions consider the real life instructor almost superfluous, have a look at this story of a class where one professor, the instructor of record, is acting as a commentator to a series of video recordings. A similar thread runs through all the interest with MOOCs and the Khan Academy: the face-to-face interaction with a human instructor is downplayed.

At higher level courses, things can be a little different. I have greater freedom in deciding what content to teach. But even then, there are few cases where I think that what I have to offer in a class is unique. I teach a neurobiology class where I had complete creative control. That’s great. But at the end of the day, there are neurobiology and neuroscience classes all over the country, and “I took neurobiology at university X with instructor Y” is not that indicative of a unique experience.

But research? There are not other people doing the studies I do. There are not other people writing the papers I write. My research remains hand crafted, not mass produced. Research is entirely my own work in a way that teaching rarely is.

Additional, 8 January 2015: Siobhan O'Dwyer riffs off this post: "Artisanal academia."

External links

Teach while you’re at it
When a flipped-classroom pioneer hands off his video lectures, this is what happens

South Padre Island winter seminar series kicks off this week!

Writing and data analysis is going very well for me right now (one manuscript revisions submitted, two manuscripts developing at a nice clip), but I wanted to stick my head up long enough to say that I’m kicking off the UTPA Coastal Study Lab’s winter seminar series this Saturday! (Click to enlarge the schedule.)

I’m giving a talk about my sand crabs, summarizing what I’ve learned over the last half a decade. (Wow, has it been that long?) I will have a lot of new stuff, including stuff I’m analyzing right now. I’m excited about it!

And 1,000 style points for those who recognize the musical reference in the talk title.

Tuesday Crustie: I like spikes!

This amphipod is probably Acanthogammarus victorii. It’s about 70 millimetres long, and found in Lake Baikal in Russia.

Photo by Olga Kamenskaya, from here. Hat tip to Rob Camp and Miss Mola Mola.

2014: fruitful and frustrating in equal measure

I worried that I would never had a professional year as productive as 2011. I had six papers that year. I'm super pleased I matched my 2011 record this year, with six papers out again, four of which were data-driven papers.

The year started crazy, with the parasite symposium I co-organized with Kelly Weinersmith being a big success at the Society for Integrative and Comparative Biology meeting. What I thought would result in one paper turned into three. And a few other manuscripts deadlines on top of those meant that I had my door closed a lot of the first part of the year.

I had two papers that, according to their altmetric scores, were more widely seen and discussed (post-publication peer review and crowdfunding) than anything I've ever written.

But I was also frustrated. For one, I could have broken that 2011 record by a couple of papers.

One paper, whose publication seemed to occur in geological time, came out this year... but it has a 2013 publication date on the article, because it was supposed to come out at the end of last year. So it doesn't add to annual tally in my CV.

Then, I had a paper that could have been out in November. But it didn't make it out because my institution couldn't pay the publication fees on time. It's now scheduled for March.

My frustration was compounded by my apparently inability to get manuscripts off my desk and into the hands of editors in the latter part of the year. In this quiet week between Christmas and New Year's, I made good progress on revising one long-suffering manuscript. Now if I just can get a couple of other manuscripts started, which have data in the can and ready to write up... maybe I'll start feeling more productive.

Personally, it was a year of many unbloggable changes.

I am hoping that a habit of a productive person is to think about not just what you have done, but what you could have done better. And there was a lot I could have done better.

The big news on the horizon for 2015 for me is easy to pick. My current institution, The University of Texas-Pan American, is abolished and we will see the start of University of Texas Rio Grande Valley. I expect all manner of craziness to ensue as part of the creation of the new university. We have less than a year to go, and there are huge amounts of things that haven't even been close to being decided.

Related posts

All downhill from here?
In the hands of editors now

Comments for second half of December, 2014

Terry McGlynn makes the case that professors shouldn’t be sharing student gaffes.

Tuesday Crustie: Albert

This is Albert Girther (left), held by Forrest Galante (right). This story is simultaneously cool and depressing. On the cool side, it’s wonderful to see such a charismatic beast. And I’m pleased to report this specimen was returned to the wild. It’s depressing because the story notes that lobsters of Albert’s size were once common. The big ones are rare now, thanks to fishing.


External links

This giant 70-year-old lobster looks like ‘Alien’
Forget jaws, here’s CLAWS! Diver manages to land 12lb lobster reckoned to be SEVENTY years old... and takes it home to meet the dog (Dear headline writer, spiny lobsters have no claws. Did you even look at the pictures you posted?)
Large Lobster Gets Second Chance at Life

The science of asking

Holidays are a time for opening things (like presents)! Today, I want share my latest experiences in open science, involving the recent paper I co-authored (Byrnes et al., 2014) about science crowdfunding and #SciFund. I was very pleased to see it land on the front page of PLOS ONE when it was released:

While I’ve been a supporter of open access, I have never quite gotten on board with what some have called “open notebook” science: posting the data as you go. For me, there are too many distractions and dead ends in an ongoing project. I would much rather wait until I have a complete story, all ready to be tied up in a bow in a published paper.

The #SciFund project, however, was much different. I got involved shortly after round one closed. I think it was the morning after it ended. Someone (for the life of me, can’t find it) posted an initial analysis of the round one projects: how much money they’d raised, donors, the project description length, and so on. I took that, gathered even more data, and shared it as a spreadsheet on Google Docs. Someone (Jarrett Byrnes, I think) then took that data, and archived it on Figshare.

I did the same after round two. And again on round three. And four. I stayed up quite late a couple of times so that I could collect the social media data (tweets and Facebook likes) from the Rockethub website as soon as the projects closed out. And I archived all that data, again, on Figshare.

So this time, all the data was public from the start.

Then, Jarrett and I blogged about what we were seeing in the data on the #SciFund blog. For instance, here’s one by me comparing the three rounds, and here’s one where Jarret admits that the model he developed to explain success in Round 1 didn’t explain success in Rounds 2 and 3:

(M)y first response was to freak out a little bit on the inside. I mean, have we been wrong this entire time? Have I been talking out of my scientific butt? Or did I get something deeply and fundamentally wrong.

The published paper reminded me of how long in the making this thing was. It was submitted in the middle of June 2012, and was published December 2014. This is the second time this year I’ve had a paper that took well over two years to make it to print. Unlike the first case, which was due mostly to delays on the editorial side, the journal and the authors both contributed to this delay. First, like the Southwestern Naturalist situation, the PLOS ONE editor initially handling the article went AWOL on us, and we had to find a new editor. Second, we authors were not always prompt making our revisions. Coordinating four authors can be tricky, and I can testify that we all worked on this thing. There are no gift authorships here!

After we had submitted the manuscript to PLOS ONE for review, we had a reasonably complete draft of the manuscript, and we submitted it as a pre-print to the PeerJ pre-print server.

What did I learn from this experience with doing the analysis out in the open?

Journal pre-publication peer review still matters

Plenty of people had chances to comment on our work, particularly after it was deposited in the PeerJ pre-print server. We did get comments on the pre-print, but the journal reviewers’ comments were more comprehensive.

Maybe we just got lucky with our reviewer. But, others have also expressed the opinion that people are most liable to act as peer reviewers when they are being asked to do it for a journal.

Publishing a peer-reviewed journal article still matters

By the time the PLOS ONE paper came out, I’d spent several years blogging about #SciFund here at NeuroDojo, on the #SciFund blog, and talking a lot about it on Twitter and other social media. The pre-print is very similar to the final published PLOS ONE paper. I worried nobody would pay an attention to the PLOS ONE paper, because there was not a lot there that we had not already talked about. A lot, I’d thought.

Boy, was I wrong. The altmetrics for this article quickly rose, and are now tied with my article about post-publication peer review from much earlier this year.

The word of mouth was helped by Jai organizing a press release through University of California Santa Barbara. (I tried to interest my university in putting out a press release. Silence from them.) That helped generate a reasonable number of pointers to this article on Twitter.

We also tried making a video abstract. It has a couple of hundred views now, which is not horrible.


And we did a panel discussion the week after the paper was released, too:


Following the panel discussion, the #SciFund paper rated an article on the Nature website.

But even among my regular followers, people who I thought might have looked at the pre-print, were commenting on the published paper. The pre-print didn’t get the traction that the final published paper did.

An excellent example of this is that we had one detailed comment picking apart Figure 8 in the PLOS ONE paper. Someone could have made this comment at the pre-print stage – this is one of the usual arguments for making pre-prints available. But the PLOS ONE comments feature isn’t used that often, so my reaction to the criticism was kind of summed up thus:

We’re still trying to figure out how to respond formally. Should we try to issue an erratum to the figure? Just post a corrected figure in the comments? But here is a new version of the figure:

Being open and sharing data is a good thing to do. But my experience with this paper suggests to me that the “screw journals” approach is not ready for prime time yet. And this was a project that, in theory, should have been a good one to try the “just blog it all as you go” method of sharing science. #SciFund was born and raised online. It exists because social media exists. I would have expected this paper to have reached its audience well before the final PLOS ONE paper came out. But all the blogging, tweeting, and pre-prints did not equal the impact of the actual journal article.

I am pleased this article is finally out. But we still have analysis from round four of #SciFund, and we are starting to eye round five, so I don’t think this will be my last crowdfunding paper.

Reference

Byrnes JEK, Ranganathan J, Walker BLE, Faulkes Z. 2014. To crowdfund research, scientists must build an audience for their work. PLOS ONE 9(12): e110329. http://dx.doi.org/10.1371/journal.pone.0110329

External links

Crowdfunding 101 (Press release)
Crowdfunding works for science
Secret to crowdfunding success: build a fanbase
Do pre-prints count for anything?

Hat tip to Amanda Palmer, fellow traveler in crowdfunding, whose book title inspired this post’s title.

H.E.B.’s donation to UTRGV: the gift that keeps on conflicting

This was the scene last week, when H.E.B., a chain of grocery stores that runs through Texas and Mexico, donated a million dollars to the planned new UTRGV South Texas Diabetes & Obesity Institute.

It’s all very festive and season and everyone is playing off the Santa theme.

My reaction was more like this:

The H.E.B. donation creates a possible conflict of interest for UTRGV researchers.

Let’s start by stipulating that where money for research comes from matters. There is a large body of research on this. Ben Goldacre has documented a lot about the relationship between corporate funding and research results in his book, Bad Pharma. Here's a soundbite that is close to the bottom line (emphasis added):

(I)ndustry-funded trials are four times more likely to give a positive result than independently sponsored trials.

Given that the source of research funding can affect what results are ultimately published, what are possible problems here?

H.E.B. is part of the food industry. They don’t just distribute and sell other people’s food, either: they have their own in-house brands. This means they have vested interests in research results on diabetes and obesity. What they make, what they sell, and how their stores are laid out (their checkout isles are loaded with soft drinks and chocolate bars), all have implications both for their profitability and for public health, as this paper notes:

Retail food environments are considered influential in determining dietary behaviours and health outcomes.

On the surface, it’s hard to tell if this donation was made because H.E.B. wants to be on the right side of this issue, or whether it’s a public relations whitewash that is cheaper than actually changing their business practices in the service of public health.

Even if the donation was given in good faith, the H.E.B. donation may strongly influence the kind of research questions that the Institute can ask.

The South Texas Diabetes and Obesity Institute hasn’t published any research yet, but a research team has been recruited. It’s to be led by Sarah Williams-Blangero, whose CV lists her research interests as genetic epidemiology, infectious diseases (which diabetes is not), genetic management, and nonhuman primate genetics.

“Diabetes” and “obesity” are notable for their absence. In fact, out of over 100 publications listed on her CV, not one mentions “diabetes” or “obesity”in its title.

How interesting.

So what will the Diabetes and Obesity Institute publish research on? It isn’t clear yet, but it does not look good for someone who wanted to study the health impacts of certain kinds of food availability, social influences, advertising, and so on.

There have been cases like this before. American Academy of Family Physicians got sponsorship from Coca-Cola. The American Dietetic Association was criticized for accepting sponsorship from Hershey’s, the chocolate maker. This post on the latter mirrors my concerns:

I don’t doubt that the ADA has good intentions- they likely perceive sponsorships as potential to change corporate behaviors, working with them instead of against.  But it is a huge conflict of interest, and there is a high risk that the companies will use the partnership to improve their image - here is Hershey already using it (and RDs) to tell the public that their chocolate products are ok - never-mind doses or which types, or the other ingredients that may come with it.

In an email, Travis Saunders (who blogs at Obesity Panacea) noted that the food industry often funds research related to obesity in some way (particularly exercise), but that there are no particular guidelines for health researchers in navigating the potential conflicts of interest. That there are no guidelines doesn’t mean everyone’s okay with this: there is contention among research in the area.

What would I like to see done about this? I am not saying that UTRGV should give back the money. First, I would like to see any research coming out of the Institute list the H.E.B. funding, and include it in their “conflict of interest” section in every paper and poster they publish.

Second, I want a real discussion about this among the university community. I find it a bit disturbing that they made this announcement in the week after final exams, when many students and faculty have already left campus, and there is not probably going to be much chance for discussion in university bodies like the faculty senate until late January.

UTPA and UTB were mainly teaching institutions, and did not get large amounts of research money. But as we transition to UTRGV, and to becoming a research university, we may need to give a lot more thought to what are acceptable funding sources and conflict of interest guidelines.

It’s not fun playing Grinch to this announcement, but maybe it is necessary. This may be more of a lump of coal than a gift.

Additional, 29 December 2014: Fit Academic adds some more perspective (lightly edited):

Hard, because much obesity and diabetes research funded by food or pharma. Invited to collaborate on grant funded by Coke. Said no, but funding is limited. Sometimes it’s food and pharma money or no money at all.

Conflict of interest isn’t an all or nothing thing; there’s obviously gradations. I think the next question is, how do we manage these possible conflicts? I think full disclosure is a good first step.

Update, 8 March 2016: I haven’t forgotten you, sucker! Vox magazine has a good article about how the food industry influences research.

Related posts

Protesting ethics 

External links

Obesity Panacea blog
Expanding the Definition of Conflict of Interest - Big Food Edition
A note on the ADA, corporate sponsorship, and PepsiGate

Pics from H.E.B. presentation here and here.

Tuesday Crustie: Merry Crust-mas!

Whether outside your home...

Or inside...

May you all carapace for one another this Crust-mas!

Wreath by Frank Gruber on Flickr; ornament by Sarah-Rose on Flickr; both used under a Creative Commons license.

Studying species you like

As an undergraduate, one of my professors recommended that you should study organisms that you like. In a new paper, Ferry and Shiffman talk about not getting that advice... in fact, they received advice that was about 180° away from it:

Scientists should not, according to this instructor while singling out DS and a student studying marine mammals as examples, pick a species that they “like” and then come up with a research question related to it. Author LF had a similar experience in graduate school, as she was also studying elasmobranchs. Both are/were perceived as “shark-huggers,” and felt pressure to defend their study organisms.

Ferry and Shiffman mention one common reason to study a particular organism: some are just convenient. It’s convenient for neurobiologists that squid have especially large axons, for instance. This is encapsulated as the Krogh principle, after physiologist August Krogh (pictured), who codified it thus:

For many problems there is an animal in which it can be most conveniently studied.

However, convenience is not, and should not, be the sole arbiter of species that people study. In fact, Krogh himself mentioned this, in the very same article (my emphasis):

I want to say a word for the study of comparative physiology also for its own sake. You will find in the lower animals mechanisms and adaptations of exquisite beauty and the most surprising character(.)

Every person picks what they study for their own reasons. It might be the organism, it might be the question, it might be something else. None of those many reasons reasons is inherently better than any other. To pick on someone for doing science than a different reason you do is pompous.

Additional: Katie Pieper made this useful remark:

But the system must be well suited for the question.

References


Ferry LA, Shiffman DS. 2014. The value of taxon-focused science: 30 years of elasmobranchs in biological research and outreach. Copeia 2014(4): 743-746. http://dx.doi.org/10.1643/OT-14-044


Krogh A. 1929. The progress of physiology. American Journal of Physiology 90: 243–251. http://ajplegacy.physiology.org/content/90/2/243

Science crowdfunding panel discussion

Earlier today, I took part in a panel discussion on Google Plus. Here is the archive of the discussion on YouTube:


I am still working up a post about the story behind the #SciFund paper that came out in PLOS ONE last week. Stay tuned!

Tuesday Crustie: Chanukah

Do you have your lobster ready for the festival of lights, which begins tonight?

Many creeds love crustaceans. From here. Hat tip to Miriam Goldstein.

Comments for first half of December 2014

The Guardian is collecting doctoral dissertation dedications. I contributed mine.

Small Pond Science looks at reference managers. Indispensable for any academic, in my opinion.

Jacquelyn Gill has become one of the latest in the online science community to have a crack at crowdfunding. She had one of the bigger successes I’ve seen, successfully raising over $10,000. She summarizes her experience here.

I make a cameo in Kelly Weinersmith's thesis. Shucks. You rock, Kelly.

Elephants have more neurons than humans

We are always impressed by animals with large brains, because we have large brains. But, of course, even though we arguably show some of the greatest behavioural complexity, we don’t have the biggest brains, as this beautiful face reminds us.

Souzana Herculano-Houzel has proposed a simple hypothesis: the reason humans are as smart as we are is because we have more neurons than other animals.

What is it that we have that no other animal has? My answer is that we have the largest number of neurons in the cerebral cortex, and I think that’s the simplest explanation for our remarkable cognitive abilities.

“But we don’t have the biggest brains! Big animals have bigger brains! How can we have more neurons than they do?”

Herculano-Houzel has been investigating the scaling relationships between brain size and neuron number. The way brains get big differ in different groups of mammals (Herculano-Houzel 2009). In rodents, larger brains tend to have larger neurons. Primates follow different rules: larger brains tend to have neurons of about the same size.

This means that if you started with a rodent brain and a primate brain of the same size, and increased their volume by the same amount, the primate brain would get disproportionately more neurons.

This means that you can’t easily predict the brain size from one group of mammals using data from another group of mammals.

Herculano-Houzel and colleague recently published a pair of papers to test the “more neurons, more behavioural complexity” hypothesis using the elephant. First, Neves and colleagues (2014) examine the number of neurons in afrotherian mammals. The number of neurons in their brains scale with more like rodents than primates.

Although elephants are afrotherians, the analysis of their neuronal numbers comes in a separate paper (Herculano-Houzel et al., 2014). The total number of neurons in an African elephant’s brain is estimated to be three times greater than in humans (257 billion neurons compared to 86 billion)... but a huge proportion of those are in the cerebellum. And by huge, I’m talking about 97%.

The elephant’s cerebellum seems to be an outlier among mammals in several ways, but I’m not sure why. I’m not sure Herculano-Houzel or her colleagues know why, either. The “quick and dirty” function of the cerebellum in mammals is usually described as motor control, and maybe the distinctive trunk of elephants is playing an important role here.

How about the cortex, the centerpiece of Herculano-Houzel’s behavioural complexity hypothesis? An elephant’s cortex has about 5.6 billion neurons, compared to a human, which is estimated at around 16 billion.

This certainly seems consistent with her hypothesis, although I’m always a little wary of ascribing too much weight to the importance of the cortex. Karl Lashley spent a lot of time looking for the seat of memory in the cortex because people thought it must be important, and in so doing, overlooked the hippocampus in the formation of memory.

It would not surprise me in the slightest if Herculano-Houzel has whale brains in her lab awaiting analysis. Whales are the next obvious group to use these techniques with.

References

Herculano-Houzel S. 2009. The human brain in numbers: a linearly scaled-up primate brain. Frontiers in Human Neuroscience 3: 31. http://dx.doi.org/10.3389/neuro.09.031.2009

Neves K, Meireles Ferreira F, Tovar-Moll F, Gravett N, Bennett NC, Kaswera C, Gilissen E, Manger P, Herculano-Houzel S. 2014. Cellular scaling rules for the brain of afrotherians. Frontiers in Neuroanatomy 8: 5. http://dx.doi.org/10.3389/fnana.2014.00005

Herculano-Houzel S, Avelino K, Neves K, Porfirio J, Messeder D, Mattos Feijó L, Maldonado J, Manger P. 2014. The elephant brain in numbers. Frontiers in Neuroanatomy 8: 46. http://dx.doi.org/10.3389/fnana.2014.00046

Photo by Neil Hall on Flickr; used under a Creative Commons license.

Species described at UTPA

As an organismal biologist, I like to imagine discovering a new species. In the course of researching a little departmental matter, I realized that our department can lay claim to introducing three new species to the world of science: a fish, a flower, and an insect.

Garrett GP, Edwards RJ, Buth DG. 2003. New species of Gambusia (Cyprinodontiformes: Poeciliidae) from Del Rio, Texas. Copeia 2003: 783-788. http://www.asihcopeiaonline.org/doi/abs/10.1643/IA03-090.1

McDonald JA. 2008. Merremia cielensis (Convolvulaceae: Merremieae): a new species and narrow endemic from tropical Northeast Mexico. Systematic Botany 33: 552-555. http://dx.doi.org/10.1600/036364408785679833

Terry MD, Whiting MF. 2012. Zorotypus novobritannicus n. sp., the first species of the order Zoraptera (Zorotypidae) from the Australasian Ecozone. Zootaxa 3260: 53-61. http://www.mapress.com/zootaxa/2012/f/z03260p061f.pdf

Plus, some of our faculty members described a new snail species, although that was work she did before they joined our department.

Perez KE. 2011. A new species of Praticolella (Gastropoda: Polygyridae) from northeastern Mexico and revision of several species of this genus. The Nautilus 125:113-126. http://www.northamericanlandsnails.com/publications/The_Nautilus_125_113-126.pdf

DeYoe HR, Stockwell DA, Bidigare RR, Latasa M, Johnson P, Hargraves P, Suttle CA. 1997. Description and characterization of the algal species Aureoumbra lagunensis gen. et sp. nov. and referral of Aureoumbra and Aureococcus to the Pelagophyceae. Journal of Phycology 33: 1042-1048.

Picture from here.

Tuesday Crustie: But wait, I’ve got a better plan...

... to catch this big red...

Watched a lot of Voyage to the Bottom of the Sea after school when I was very young. So much so that I don’t remember much of it besides my enjoyment, and thinking that the Seaview was one very cool design for a submarine. And alas, I don’t remember Victor Lundin’s protrayal of the title character of this episode:

Defending the astonishingly successful

Inside Higher Education reports on a speech by University of California president Janet Napolitano, in which she tells advocates “defending graduate education.”

<sarcasm>

Right, because graduate programs are doing so poorly right now.

</sarcasm>

It is weird to hear about the need to “defend” graduate programs, when the growth of master's degrees in science and engineering looks like this:

And the growth of doctoral degrees in science and engineering looks like this:

These numbers show a higher education enterprise that is thriving, not in need of defense.

Yes, it’s true these data are only for science and engineering, but I have no reason to think those for other disciplines are dramatically different. Plus, when you read Napolitano’s comments, it’s pretty clear that she is mainly talking about economic competition in the scientific and engineering fields. For instance:

640 startups are based on inventions created within the University of California, she added(.)

And two of her three “grad school success stories” – success anecdotes, really – are about STEM disciplines (medical research and information technology).

And Napolitano trots out the hoary promise that huge numbers of academic jobs are going to open up:

(T)he state is projected to need tens of thousands of new professors as the baby boomer generation retires.

Yeah. I heard those projections before I started graduate school in the late 1980s. Yet somehow, over and over again, they never materialize. And let’s say the number of academic positions available per year in the United States doubles. Following the trend lines in the graph above, doctoral recipients are still going to outnumber faculty positions by three or four to one.

Napolitano is a politician with vested interests. It is in the interests of universities to lobby for more funding to support more graduate students. It is in the interests of universities to portray grad school and grad students as benefiting the greater good (which it does, by the way). And it is in the interests of universities to say that problems with a shortfall of employment opportunities are going to go away.

But Napolitano is lobbying for money, not defending something that is under threat in any meaningful way.

External links

Defending graduate education

“We should celebrate scientists... They are brave.”

Many are sharing this superb New York Times article on the woman who discovered the chemical francium. There are only just over 100 elements, and some were known to the ancients, so being the discoverer of a chemical element is a rare achievement indeed.

The article has a lot to offer. It’s part biography about one remarkable woman. It’s part indictment of scientific sexism of the past, lax attitudes about safety, and more. But I want to pull out this section near the end, which talks about science generally, which I liked a lot:

We should celebrate scientists not solely for their accomplishments but also for their courage and the tenacity required to discover anything at all. There are brave people out there working right now. They are brave not because they are killing themselves slowly or leaping from airplanes or catching rare tropical diseases, although scientists have done all those things. They are brave because of the intense emotional risks of trying to do something no one has done before by following your own lead. Radiation is a potent allegory for human life. Everything is always, inevitably falling apart; we are all in arrested decay. Our greatest achievements may become at best footnotes; few people remember us; we can’t know what will eventually come of our work.

External links

My Great-Great-Aunt Discovered Francium. And It Killed Her.

Tuesday Crustie: Chindōgu

I normally don’t emphasize the use of crustaceans as food in this feature... but... but... this cooking technique must be seen to be believed.


Hat tip to Jarrett Byrnes, via Gawker.

Build your brain by losing that gut

The old joke goes that places with terrible weather are made that way so only the best people live there. Dullards can’t hack it.

This little guy shows there may be some truth to that.

This is a black-capped chickadee (Poecile atricapillus). It’s a small bird that ranges over much of North America. Because it has such a wide distribution, the birds that live in different areas are slightly different from those that live in other areas. A recent paper by Kozlovsky and colleagues takes advantage of that to test an idea about brain size.

The expensive tissue hypothesis is an idea that says if you have more of one kind of expensive tissue (like brains), you will either have to:

• Increase your overall metabolic rate to pay for the extra tissue.
• Give up something. The original paper suggested that the gut was a prime candidate for reduction when brain size went up. It was also expensive, and you could compensate for a small digestive system with higher quality food.

A few papers have tested this, but this one is nice because it is all a single species. Kozlovsky and colleagues show nicely that the bigger the brain in the chickadee, the smaller the stomach and gut. This cleanly fits the expensive tissue hypothesis.

Heart size, on the other hand, does not correlate with brain size in any way. Again, this fits the original formulation of the expensive tissue hypothesis,  which predicted that heart muscle would be unaffected by brain size. The need to pump blood kind of limits how much you can reduce heart tissue.

What was a little less expected was the influence the climate had on the birds.

The birds living in cold climates, like Fairbanks, Alaska (pictured) had bigger brains, and smaller bodies, than those living in more moderate, easy-going climes. Either one might be easy to explain on its own, but the combination is unexpected. Usually, both body size and brain size go up hand in hand (or, in this case, wing in wing). It’s not entirely clear how this is happening, although it certainly suggests there are some strong weather-related selection pressures shaping both features.

One factor that might be coming into play is that chickadees are food caching birds, and cold weather may actually allow the northern chickadees to store higher quality food for longer. The Alaskan chickadees live in a deep freeze, as it were, that lets them store insects and such for longer, because the cold weather means they don’t rot.

Just when I was finishing this blog post, I saw this tweet:

Completing a PhD requires brains, guts, perseverance(.)

But... but... if you have more brains, you can’t have as much guts! It reminded me of another old joke: “Good. Fast. Cheap. Pick two.”

Reference

Kozlovsky DY, Branch CL, Roth II, TC, Pravosudov VV. 2014. Chickadees with bigger brains have smaller digestive tracts: a multipopulation comparison. Brain, Behavior and Evolution 84: 172-180. DOI: http://dx.doi.org/10.1159/000363686

Bird photo by Rick Leche on Flickr; winter picture by Curt on Flickr; both used under a Creative Commons license.

Comments for second half of November, 2014

Worth talking about on the web...

I make a cameo in SV-POW on the future of music and academic publishing. I show up in the comments, too.

Jon Tennant reviews a recent open access conference.