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. To 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

27 January 2016

A weapon of delight instead of harm

This is a pure delight, guaranteed to lift any day.


So worth carpet bombing my social media feed for. Hat tip to John Wick.

External links

This 200-Year-Old Ridicoulsly Ornate Pistol Has a Hidden Secret

Fluctuating publication costs

Savraj Grewal was bemoaning that it would cost Canadians CAN$7,000 to publish a paper in the open access journal Cell Reports. Lively discussion about this followed on Twitter.

Here’s how Cell Report’s cost stacks up to other open access journals. You have to break the axis to compare it to most other journals.



My first reaction was, “Why would anyone pay this when they could publish in PeerJ for a tenth of the cost?” There are a lot of open access journals, so what are people criteria are authors using to distinguish between them? I don’t understand how people pick between Nature Communications (US$5,200), Science Advances, or Cell Reports. They’re all open access versions of existing “brands,” but I don’t know if they genuinely provide difference services. I don’t think they do. And providing the publisher name is the only service they provide that PLOS ONE, PeerJ, and a wide variety of other journals don’t.

Then I realized the cost to Canadians is not purely a function of Cell Press’s higher than normal article processing fees. The Canadian dollar is weak right now (0.7109 USD, according to my quick trip to CBC).

I don’t think I’ve seen discussions of open access fees and publication costs that have acknowledged currency volatility. When the cost of a publication is in US dollars, minor changes in exchange rates can make big differences in a researcher’s budget. Especially when the cost in as high as Cell Reports.

I’m not sure if anything can be done about that.

Update: Because I can’t stop plotting things,  here’s the how the big three biological publishers’ open access journals stack up:


Related posts

The sticker price on AAAS’s Zune journal 

External links 

Eigenfactor

25 January 2016

Journal circulation and citations

Stuart Cantrill, writing at The Chemical Connection blog, had this plot showing the citations of one article that was published in multiple venues:


The point is that citations are often used as a measure of the quality or impact of a paper. But since this is the identical article, “article quality” cannot explain the variation in citations. Stuart hypothesized:

(P)erhaps more people read the New England Journal of Medicine than the Medical Journal of Australia and so a wider audience will likely mean a wider potential-citation pool.

I left a comment that this should be testable, because magazines (American ones, anyway) were required to disclose their print circulation annually. Well, one thing led to another (“another” in this case meaning, “a bunch of Google searches for ‘[Journal name] print circulation’”). I couldn’t find the circulation figures for the Croatian Medical Journal. Here are the results:



I’m surprised. For a while, I’ve been thinking about what relationship there is between a scientific journal’s readership and its Impact Factor. It seemed to me that Impact Factor might just be a proxy measurement for readership. So, I genuinely expected the correlation would be similarly tight as the one Stuart had for Impact Factor.

Of course, these circulation figures are mostly based on printed copies distributed. This confuses the issue for many reasons. First, a print issue can be read by many people. Nature estimated about eight people read one copy of their journal. Plus, print is drying up as a medium for magazines and journals. It may well be that website visits or some other measure is a more important measure of a medical journal’s “readership.”

Update, 31 March 2016: Daniel Shanahan has a new paper in PeerJ that shows the same thing as Cantrill’s blog post. When you publish the same article in multiple venues, the Impact Factor predicts how many citations the article gets, which suggests that Impact Factor mostly predicts Impact Factor, not how scientifically interesting the articles within are.

External links

Imperfect impact

Appendix 1: Journal and circulation (click journal name for source of circulation)

New England Journal of Medicine: 120,000
The Lancet: 29,103
Journal of the American Medical Association (JAMA): 292,902
British Medical Journal: 121,762
Canadian Medical Association Journal: 81,083
Medical Journal of Australia: 30,706
Annals of Internal Medicine: 100,014

22 January 2016

How I’ve parasitised research

Michael Hoffman did the research world a favour by highlighting a new editorial in the New England Journal of Medicine about data re-use.

The aerial view of the concept of data sharing is beautiful. ... However... There is concern among some front-line researchers that the system will be taken over by what some researchers have characterized as “research parasites.”

Oh boy.

As a biologist, I know that parasitism is one of the most successful strategies for living in the world, and play an integral role in ecosystems. But I’m no so much a biologist that I fail to recognize that those who re-use other people’s data – like me – are being disparaged.

Following Longo and Drazen, I guess creating GenBank was totally the wrong thing to do.

I became convinced of the usefulness of data sharing when I started collaborating with Paty Feria, modelling the distribution of crayfish species. About the same time, I was starting to work on the ecology of sand crabs. Both projects required using other people’s published geographic data. I spent a long time pulling out distribution records from published papers.

Without that geographic data, we couldn’t have created the new predictive models for distribution (Feria and Faulkes 2011, Faulkes et al. 2012). Those models were considered in this risk assessment for marbled crayfish, which demonstrates that, at some level, people found those new analyses useful.

While not critical in analyses, geographic data was critical in creating maps that allowed my to show the context of a range extension (Faulkes 2014). I couldn’t really prove it was an extension without that.

Because of my experiences in creating those papers, I’ve put in effort into archiving my own data, usually on Figshare. My record isn’t perfect, but I hope it might be useful to someone else.

There are a few (very few) defenses of the Longo and Drazen piece. First, they are trying to show an example of good collaboration, where everyone was happy. That could be useful, if they had stripped out the potshots about “parasites.”

Second, they are talking about medical research, where patient consent and privacy are ongoing, real concerns that shouldn’t be swept under the table. Remember issues around sequencing the DNA of HeLa cells, and people then going, “Hey, the woman those cells came from still has immediate family, and posting those cell DNA sequences could violate their medical privacy.”

But Longo and Drazen don’t frame it that way. Instead, they frame the problem as one in which researchers could suffer embarrassment or career impediments because of someone else used their data.

The first concern is that someone not involved in the generation and collection of the data may not understand the choices made in defining the parameters.

Someone might misunderstand what I was doing and I could be embarrassed.

(S)tealing from the research productivity planned by the data gatherers...

Someone could publish before me.

(E)ven use the data to try to disprove what the original investigators had posited.

Someone might show I was wrong and I could be embarrassed.

I understand wanting to protect your reputation and advance your career. But if your reputation and career can’t stand up to someone else using you’re data, it’s not a very strong career to start with.

25 January 2016: Co-author Drazen wouldn’t comment on the use of the word “parasite” when asked about it by a journalist. But Drazen has penned a response.

References

Faulkes Z. 2014. A new southern record for a sand crab, Lepidopa websteri Benedict, 1903 (Decapoda, Albuneidae). Crustaceana 87(7): 881-885. http://dx.doi.org/10.1163/15685403-00003326

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

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

Gewin V. 2016. Data sharing: An open mind on open data. Nature 529: 117–119. http://dx.doi.org/10.1038/nj7584-117a

Longo DL, Drazen JM. 2016. Data sharing. New England Journal of Medicine 374: 276-277. http://dx.doi.org/10.1056/NEJMe1516564

External links

Attack of the research parasites
I am a research parasite. Got a problem with that?
Priggish NEJM Editorial on Data-sharing Misses the Point it Almost Made
A fundamental difference of opinion
NEJM Calls Data Scientists 'Parasites.' Can Joe Biden Change Their Minds?
Criticism of ‘research parasites’ moves NEJM in the wrong direction
On research parasites and internet mobs - let's try to solve the real problem.

Data Sharing and the Journal

19 January 2016

Tuesday Crustie: Scully, is that you?

I haven’t yet been able to figure out whether this Anderson...


Inspired this one:



Or maybe I’m just too excited by The X-Files returning.

This is Cambarus andersoni, a new crayfish species described last month. As you can see, it’s a pretty hefty crustie. I’m still kind of amazed that new crayfish species are being found in well-trodden places like the southeastern United States. This one is found in south Tennessee and north Alabama.

Reference

Jones DR, Eversole AG. 2015 Two new crayfishes of the genus Cambarus (Decapoda: Cambaridae) from Northern Alabama and South Central Tennessee, U.S.A. Zootaxa 4058(2): 151–174. http://dx.doi.org/10.11646/zootaxa.4058.2.1


Gillian Anderson picture from here.

06 January 2016

“Threats from pets” free talk next week!


I’m giving a free public talk next weekend! It’ll be held at the Coastal Studies Lab on South Padre Island on Saturday morning, 16 January. I’ll be talking about the aquarium trade in crayfish.

This will probably be my prettiest talk in a long time, because I was able to get a lot of gorgeous, jaw-dropping crayfish pictures from ace photographer Chris Lukhaup. There will be eye candy. Oh yes.

05 January 2016

SICB 2016, Day 3

This morning, I sat in the complementary talks to the neuroecology symposium, which I blogged about yesterday. My notes are not as extensive, because I had been asked to step in as session moderator just a few days before the conference started. And keeping a close eye on the clock to ensure speakers do not exceed their allotted time consumes a surprising amount of attention.

The neuroecology session faced some competition, because almost all the talks in the session were about vision, and another symposium about non-traditional visual systems was going on at the same time.

Simon Sponberg talked about how moths see in dim light. Hawk moths (Manduca) are crepuscular flower feeders, as are Macroglussum (an exceptionally agile moth) and Deilephila. All have to deal with variable light, which might even be harder than consistently dim light. 

L.J. Fleishman is looking at dewlaps in anolis lizards. As you go to drak habitats, dew laps get lighter and vice versa. The physiology of the eyes plays a role in determining the visibility of the signal. He ended his talk showing how some anoles with light dewlaps exploit not just light colour, but translucent dewlaps that allow backlighting. From the right angle, the dewlap can look spectacular.

Roz Dakin is looking at how birds use vision to control flight, particularly hummingbirds. Birds (budgies) and bees extract speed of image movement to determine distance. They steer away from vertical stripes and towards horizontal stripes. They can get hummingbirds to fly because hummingbirds have to feed so many times a day. Manipulating vertical stripes did not change hummingbird flight, but horizontal stripe manipulation made them fly up. Results were not consistent with the pattern velocity model (well established in bees). She suggested that the differences might be related to birds trying to avoid hitting the ground.

Brian Dalton asked, “What are opsins doing in the eyes of cichlids fishes when they are present in very low levels?” Coexpression seems to enhance contract and detection distance in some cases.

Michael Grace has the only non-visual sensory system in the session: he was looking at thermal imaging in snakes. A 2010 paper hypothesized that TRP channels are involved in transduction. But that was based on data from the brain of the snake, not the pit itself. Michael showed snake TRPA1 is expressed in the pit. Then they put snakes in an fMRI machine, and showed that an antagonist to the TRPA1 reduces fMRI signal to heat induced neural signal. The antagonist also diminishes the snake's thermal behaviour.

Then I gave  my talk on sand crab eyes. This project is still in the early stages, and I wasn’t happy with my talk. I haven't had a chance to pull it all together in my head yet. But I did have some questions at the end, which is always a good sign that I was at least understandable.

The last talk before I left was by I. Thanigaivalen on whether Drosophila use halteres to influence gaze control. Some previous papers suggested haltere removal should affect head movements, but this held true only in certain conditions. The visual stimulus speed matters a lot. Haltere removed flies have smaller responses in flying flies, but only at high visual stimulus speeds. When the flies are not flying, the head angles are random, both with and without halteres.

And with that, I had to start making my way to the Portland airport. I am sorry that this was such a smash and grab visit to SICB an this year. That said, even with only a day and a half, I still got some leads on an interesting potential project.

The highlight of the meeting, though, was walking up to a random poster during registration on day one. I walked up to it because it was the only poster on all the boards on the row, and I thought, “This poor presenter got screwed. I want to make sure at least someone takes to her.” And we were well along chatting about the poster when I realized that it cited a chapter I wrote. Success!

(Additional, 6 January 2016: It was this poster.)




Impressions overall: SICB is growing, and the number of simultaneous sessions feels less manageable than in the past. I think if it grows much more, it may have to start shifting its emphasis to poster sessions, like other large meetings have done.

SICB has struggled with its online presence in the past, and this meeting continued the trend, whereas some years there was practically no wifi, the convention center had wifi throughout - but you had to pay for it, and it wasn’t cheap. 

Similarly, the app was a mixed bag. It worked on my tablet but not on my phone. Because I didn’t want to pay for wifi, this made it only minimally useful. You could add things to your schedule and view it without a wifi connection (although it was slow to load) though, so it wasn't a complete loss.

Portland is a nice city, but not my favourite conference venue. There was a surprising lack of places to eat around the conference center. While SICB does have some food at its socials and such, they tend to be finger fare and small desserts, not really proper meals. Similarly, a lot of the hotels were a bit of a hike / train ride away. These didn’t facilitate the informal and serendipitous networking and conversations that are often the most productive part of a scientific conference.

Related posts

SICB 2016, Day 1
SICB 2016, Day 2

04 January 2016

SICB 2016, Day 2

(Note: These notes from talks I sat in today at SICB are largely unedited. Apologies for typos!)

I sat in the neuroecology symposium. It started with Richard Zimmer, talking about the concept of keystone molecules: those that have more impact that. You would predict by abundance, started off with tetrodotoxin, a defense molecule in salamanders.

Then, he moved on to talking about a glycoprotein used as a contact cue in rocky beaches. bArnacles seem to make it as part of their shell, which gets used as both a settlement cue by other barnacles and as a predatory cue by predatory whelks.

Moved to starfish as keystone predators, and starfish will come to a single compound, another glycoprotein. KEYSTONin protein drives predation on mussels. Take it out, and you completely lose starfish predation. There are hints mussels use the same molecule to build their shells. Closing question is how many effects described as biotic interactions are actually chemical ones.

Ashlee Rowe was next. I had worked with her before in a nonciception sympsium. She starts out pointing that many species have developed neurotoxins to interact with ion channels as defenses. One subset of these neurotoxins cause extreme pain. In particular, she is working with the Arizona bark scorpion Centroides scorpions. Their neurotoxins bins to sodium and potassium channels in neurons. The neurotoxins cause spontaneous, prolonged action potentials.

These scorpions are preyed upon by grasshopper mice, however. Grasshopper mice also eat non-painful scorpions. The mice are quite resistant to the venom, not killed, and causing little pain. The venom activates action potentials, but the signal is blocked quickly so the signal doesn't reach the grasshopper mouse brain.

But drop the mice know the difference in pain? Grasshopper mice prefer a non-painful scorpion over a painful one. But when the stingers were blocked, mice much more likely to eat the painful scorpion (when sized matched). And naive mice will go for scorpions at random - if stings are blocked. Is the stings are unblocked, the captive bred mice won't bother to attack the scorpions at all. In the real world, the painful scorpions are abundant, but skinny and painful, so there are trade offs.

Jessica Fox was next on fly mechanoreceptors. What determines a fly compared to other flying insects is that they have a sensory organ: the halteres. Haltere have 100-300 sensible at the base, which provides balance. They cannot fly without halteres. The halteres are incredibly precise in tracking the phase of their movements, up to as fast as their machine would got (150 Hz). The sensory population shows range fractionation to the phase of the halteres movement.

Some flies activate their halteres when walking. One of the most recent fly clades quite consistently move their halteres while walking. These movements are not driven by flight muscles, but by intrinsic haltere muscles. When walking, the halteres can take any phase relationship.

They created a fly Olympiad for flies with ablated halteres. The only task that haltere ablated flies had a problem with was walking up walls and falling off walls when given a surprising vibration (cup drop). Talking about mutations in "early" and "late" stages of evolution (whatever those are) in guppies. Lots of convergence in guppy phenotype. Looking at gene expression pathways in these guys.

Kim Hoke was taking about responses across different timescales. What determines the response of an animal to another member of its species at any given time. Many possibilities, but one one happens.

When lab-reared animals are reared with predator cues, several protein expressions change. She is also able compare fishes from different drainages. There is some concordance from different lineages, but there is a lot of smear. It's not a tight relationship. She is suggesting that network homeostasis could drive coordinated divergence, but this was not the case. Instead, there seems to be a few central genes in the module that are evolving quickly. Possibility are connected genes evolve in long term, but not short term. So convergence in phenotype has only moderate similarities in gene expression.

Observation around the halfway point in neuroecology symposium: both neurobiology and ecology seems to be optional in calling your research “neuroecology.”

Gabby Nevitt was studying chemical comminucation in pelagic seabirds like albatrosses, seabirds, petrels, and so on. How do they find each other to mate? Because they mate for life. They have huge olfactory turbinates and olfactory bulbs.

The major histocompatibility complex (MHc) often implication in mate choice, but very little work has been done in the wild, it tends to be underpowered, and the results are not consistent. So she went looking at MHC a storm petrel, which is a very common bird.

Having examined over 1,000 birds, they are seeing a lot of long tails in the alleles I in the population. But there is no assortative mating based on MHC in the petrels. There are a lot of underpowered studies out there, contributing to controversy.

They have also developed a chick choice assay, based on fake nests. Chicks can tell their parents' scent, and pick it over an MHC matched scent.

Jeremy Niven is looking at energy efficiency of potassium channels in eyes. Wants to know the trade off between energy consumption and information fidelity. The cost of action potential is related to movement of ions across the membranes: in particular, the long term potassium sodium pumps.

The size and shape of action potentials vary significantly in their energy cost. Squid action potential is wasteful! Spending way more energy than it needs to. Cortical relay cells are very efficient.

The overlap between sodium and potassium currents is a major driver of the energy costs of neurons. And neurons vary a lot in this regard.

To address this, Jeremy looks at fly photoreceptors. These neurons are non-spiking. They can respond to single photon, very little signal at low light, and reasonable signal in high light.

If the fly photoreceptors process more information, they pay a high energy cost. Modeled ATP costs per bit. Big flies can get up to pretty high bit rates, but high energy costs, too. Slow and fast photoreceptors also have different properties.

Why have a voltage gated potassium channel in the icky photoreceptor? By changing the resistance of the cell membrane, because the amount of membrane in a photoreceptor is constrained. Potassium channels are improving bandwidth and lowering energy costs. Eyes pull back on maximum information, and save huge amounts of energy by doing so.

Michael Markham was looking at metabolic costs of communication signals. For bats and electric fish, you can’t stay quiet without going “blind,” because communication is linked to sensory signaling. The cost of an action potential is a cost for sodium: 1 ATP for every 3 sodium ions.

Weakly electric fish modulate their electric organ discharges to save energy between day and night, or depending on social system. But some fish generate hundred of discharges every second it is alive. Eigenmammia terminates it action potential with a sodium gated potassium channel. Seems to be a mechanism to reduce overlap you see in sodium and potassium currents, which is wasteful. 30% more efficient was predicted.

The cost of the electric organ discharge is one of the most expensive known in the animal kingdom. You can see increases in amplitude depending on when the anime is fed. Food pumps up the amplitude of the signal, but this is not due to an absolute energetic limitation. It seems to be modulated by leptin.

Next question is how do the ion pumps keep up with the demands for ions of the channels running the action potentials? There are a lot of them, for one, but they are probably still not enough: there are probably specialized high volume sodium/potassium pumps.

Markham proposes that electric fish could be sentinel species for climate change, they are living on the energetic edge to live in these muddy waters. They are probably going to be very sensitive to changes in primary productivity.

Jeff Riffell is looking at insect olfactory neuroecology. The interaction between plants and pollinators have huge, community wide effects that structure communities. Sometimes, the communities are wide, with many pollinators per species, but sometimes it is more specific.

Platanthera are interesting orchids, for which some are mostly pollinated by mosquitoes (which is unusual), while some are flies, moths, etc.. How do their scents cause pollinator attraction? You can make good predictions about what pollinates a species based on what odor chemicals the plant is generating.

Of the mosquito pollinated orchids, only 3 species of mosquitoes act at pollinators. The odors seem to be very specific attractants.

Giving the odor to a flying mosquito in the lab changes the flight behaviour of mosquitoes: they “surge” in wing eat frequency. They respond to the scent of a moth-pollinated orchid scent by slowing a bit, although it smells much more intense to a human.

There are some antennas lobe neurons that respond very strongly to the orchid scents, while others are suppressed. The population of neurons are able to generalize between the mosquito attractive scents versus other scents, like moth pollinated orchid scents.

Marie Suver was looking at visually guided flying in fruit flies. VS and HS cells are visual neurons that seem to detect self-motion. She was able to characterize their responses to pitch and roll, and the ehnext step was to track what happened downstream from those. She found several neurons whose response was predicted by the tuning of the HS and VS neurons.

The descending inter neurons, in turn, cause various body responses, each of which is a various body axes. You see similar patterns in several vertebrates, including pigeons and rabbits, leading to some speculation that this is a common control system.

Emma Coddington looks at cortisol in salamander clasping. Vasotocin seems to be criticized cal, acting as a gate to all sensorimotor activist in clasping. Cortisol released by stress stops the clasping related behaviours.

The timing of these two hormones, and clasping, matters. The hormone or behaviour changes the salamander's response to stress (cotrtisol).

In thinking about this, she found there were limitations to thinking about time frames. Usually people just called them acute and chronic treatments. Chronic in particular was ill defined and confusing.

Cortisol interferes with the endocytosis of vasotocin in a seasonally-specific way. In no breeding animals, cortisol does very little, but has bigger effects in breeding season. Cortisol also effects brain regions differentially, as you'd expect.

Corticosterone does not affect intrinsic neural properties, but seems to tweak synaptic communication.

Hannah Ter Hofstede asks how a new signal can evolve? After all, you normally think of a sender and a received, and "signal" implies adaptation. Not incidental. There can be precursors to new signals in either a sender or receiver. But the sensitive should exist before the evolution of a signal. A sender is generally not expected to make a signal similar to a predator, say, but rather to exploit something a receiver already finds attractive.

One group of crickets, the eneopterans, produces very high frequency calls though, that normally would be categorized by crickets as an aversive bat-like sound. These female crickets don't walk towards male calling songs; the male approaches the female, who produces a brief vibrating after each male call.

Crickets will fly away from high frequency sounds, and when standing on the ground, all crickets tested show a startle response to a high frequency sound. This could be a precursor to the female "push-up."

The scenario is that males exploited female startle, so they didn't have to wait for females to come to them. Females no longer produce startle response to just any high frequency sound; it has to be the specific timing that males make. So it's now a true signal.

The females responses are tuned to about 12-15kHz, roughly that of AN2 bat detector in most species. The neural responses... Did not see any response to 5 kHz, seeming to imply AN1 is inactive or lost. AN2 type responses seemed fine. But it's not clear if the ascending neurons, especially, the AN1 homologous, are lost or just modified. All the ascending neurons respond up in righ frequency.

Exploiting predator cues may be more common than wet bought, starting off as a way for sender to exploit the receiver.

Later that night, away from the neuroscology symposium, Vincent Careau give the George Bartholomew lecture. I was grumpy about his characterization of crayfish as non-charismatic, but oh well. He was interested in the evolution of physiology, and how physiology affected evolutionary patterns. Are physiology I, performance and behaviour related in evolution? Are these complex traits evolving in a correlated way?

BMR varies by six fold even after you take body mass into account. There are a lot of explanations for this, but one might have been overlooked is behaviour. Used an open field test used in psychology, and found BMR was negatively correlated with open field behaviour.

His first species though, showed no clear relationship between the two, but later, once pedigree was taken into account, there did seem to be a correlation between the two. So how were these apparently contradictory results? It looks like it may be a species specific effect.

Next project was looking at effects of botflies on a chipmunk population. Botfly larvae on chipmunks was correlated with high BMR. Botfly infection also caused reduction in overwinter survival. If a chipmunk ever had more than 4 botflies, they didn't survive. Suggests that this is due to a reduction in oxygen consumption ability me which chimpmunks need to come out of torpor.

Careau next talked about selection for wheel running in mice. In 20 generations, selected mice run three times as much as control lines. But after generation 20, there seemed to be no increase in wheel running, suggesting there is a selection limit.

He hypothesized that wheel running on days 1-4 might constrain wheel running on days 5-6. Selection was apparent over 10 generations.

As an aside, he showed the equipment that has been used to gather the wheel running data, the experiment was started in 1993, and is still running on the same equipment: a DOS PC and floppy disks.

SICB 2016, Day 1

Portland decided to snow the first day of SICB in the morning, which turned into freezing rain by the time of the plenary talk in the evening.

The opening talk was "The biology of big" by Terrie Williams. Triggered to be a biologist by Life magazine cover on "The Great Cats of Africa" in January 1967. Gave a shout out to all the great mentors she had (all men).

Started with American mink, and she was terrified of them. Moved to swimming otters, then seals, then dolphins, then killer whales, all to figure out their oxygen consumption and metabolism.

Everything she measured was above the Kleiber curve for terrestrial mammals oxygen consumption. Reason being that carnivore is expensive. What was driving the high cost for these animals?

Showed pictures of a polar bear on a treadmill, Tasul, who is from the Portland Zoo. Had video of what bears do to treadmills, who want to tear apart everything. First day of turning the treadmill on. Bear was walking in three inch steps to "Gonna Fly Now" from Rocky.

Cost of swimming, running, and flying is similar for all mammals. That was a surprise. A swimming seal has the same cost of transport as a running dog of same size. Used analogy that all of these animals are using the same engine. You have to be concerned about the net versus total energetic cost.

"The entire planet was being driven by how much these big, hungry, carnivorous animals were eating." The top predators have a profound impact on the ecosystem.

Example: where did all the marine mammals in the Aleutians go? Looked at Stellar sea lions to figure this out, and the numbers kept going down. Orcas ate ten times the amount of a large shark. Could they be responsible for the domino effect of large marine mammals disappearing? Their metabolic rate was about three times that of other marine and terrestrial carnivores.

The caloric content need to stay alive is enormous: 200-300,000 kcal a day. This means 5-7 otters a day. Keeping a single pod alive could account for all the missing sea otters.

The whaling industry took out the key top, high energy food for orcas. So they ate down the food chain - at least that was the hypothesis. How could foraging costs be assessed in the wild? Technology with accelerometers and cameras and such made it possible.

With this technology, they learned marine mammals cheat, and do as little as possible. Energetic costs are also about defending resources like air holes. Looked for the same idea of breathing holes in narwhals. Narwhals are pure endurance animals - they couldn't swim fast if they wanted to. "I didn't believe narwhals existed, so I didn't know how we would measure its heart rate."

Narwhals love in a "landscape of fear." They are very sensitive to disturbance, which is mainly humans. Their heart rate drops down to 3-4 beats a minute. "This is like paralysis for an animal."

The changes in ice are bad for the narwhals, because it's not only the ice thinning, but piling up.

After 50 years, finally got to study lions in Africa. "This was truly a dream come true." The question was chat are the impact of lions on the local prey, and can humans live with lions?

Accelerometers are so good now you can see each paw hit the ground in the records. Can track an entire kill from an accelerometer trace, and get the size of the kill from the remains.

So can we predict lion predation events to prevent human/lion conflict?

Worked with a great tracker to find a lion, Kichaka. "I did something very unscientific. ... I just had to touch every inch of this lion." They now have 7 males, 19 females and young. You can follow them on africanlions.org. They are trying to see which males are pairing together.

They can figure out whether stops are rest points or feeding points to prevent retaliatory killing. Lots of time spent talking to herdsmen to figure out why, are kills lions or hyenas, etc. Sometimes the herdsmen are at fault for not bringing cattle in.

The bottom line: measured costs of hunting are about two and a half times expected from modeling. It's costly to be a big predator, because of different terrain, etc.

Kichaka died on Christmas. The collar will probably tell them what happened to the lion. But after 50 years, it's heartbreaking to see this happen to an animal. These things are happening every day, they just happened to record it.

There is also very little money for large animals. "It just isn't transformative." The highly endangered Amur leopard has 25 papers over 50 years. "How can we save them when we don't know how they work?" Her work was funded a lot through NSF Polar - which ended up on the #3 on the congressional wastebook. She shot back with a LA Times editorial, which mostly ended it. Except she got a FOIA from Lamarr Smith.

So why bother? You have to dig deep and go back to where you started. "tHere is nothing more rewarding and exciting than exploring nature."

This morning, she learned that one of her lions, Davey, just had cubs. "The ones saved."

She's asked by the media all the time, "What good is this?" Plays a video about the race against extinction, showing many examples of her research used in protecting endangered mammals. 1980s , start. 1990s, climate change. 2000s, age of endangered mammals. 2010s, never say die!

31 December 2015

So what happened this year?

In this, the mid-point of the second decade of the twenty-first century (which is still awkward because it doesn't really have a name... nobody calls it the “teens” or anything), what happened for me professionally?

When the year started, I was an associate professor at The University of Texas Pan American. When the year ended, I was a professor at The University of Texas Rio Grande Valley.

I made up a word. And, shockingly, people noticed it. Make you cite this post when you add “kiloauthors”, Oxford English Dictionary!

I saw a rock fall out of the sky!

My name was on the cover of a time travelling book that arrived in print this year, even though every place in the book says it was published in 2016.

My little presentation ebook I self-published got reviewed by the awesome Natalie Morales (who’s the best reason to watch The Grinder) and was translated into Russian.

I wrote or contributed to some review articles.

But I was happiest about publishing three reasonably big data-driven papers this year (plus a note): one with the most direct test of the “lobster in the pot” problem yet, one on beautiful giant neurons in shrimp, and one the crayfish pet trade. And two of them were all me. I’m happy that I still collect my own data, and not just write grants and supervise other people’s research. I want more like those in 2016, please!

But it’ll be tricky. Currently, the only thing I have in press is a chapter in the forthcoming Science Blogging book. Data collection on two projects is officially complete today, but there are, of course, lots of other teaching and service tasks to do.

Note to self:


28 December 2015

Time policing

Are you reading the blog post from your home or your office?

It’s the start of the week between Christmas and New Year’s. There is a lot of discussion on my social media feed today about academic work, I think prompted by this tweet:

Quick test to see if you're going to “make it” in academia: Are you working this week?

As advice, it’s dumb. Whether you’re working this week is no test of whether you will be a successful academic. Lots of people might work this week, but work on the wrong things. Like writing a blog post instead of that NSF pre-proposal... but I digress.

As a joke, it’s mean. It suggests overwork is the norm in academia, and that if you’re not working now, you are obviously inferior.

Academia has a deep and sometimes oppressive culture of overwork. There are many examples on this blog. There was Scott Kern saying colleagues lacked passion because research labs were empty on evenings and weekends. More recently, Eletftherios Diamandis wrote about how he worked sixteen hours a day, left childcare to his wife, and had his kids playing in the lobby and eating food from the microwave – and this was in a career advice column as an exemplar of success.

Put that attitude together in a person whose position gives them a fair amount of power and minimal oversight – like someone in charge of a grad student or post-doc – and you have the potential for stressful, terrible situations where people work like dogs because they think there is no alternative.

That said... I am a bit concerned by the potential for time policing that’s hinted at in the reactions to this tweet, and in similar situations.

First, a lot of people outside of academia have to work the week between Christmas and New Year’s. For most people, suggesting that you work this week is not something that only a Dickensian factory owner would say. That is is even an argument could contribute to the perception among non-academics that academics are overpaid, lazy fat cats.

Second, we should be careful about criticizing academics who do choose to work this week. There are many reasons to do so.

I have animals that need feeding and looking after. It’s my job to look after them. I don’t like the implication that I’m contributing to a workaholic culture because I’m doing animal care.

There are also externalities that work against taking this week off for many people. For instance, for biologists, the Society for Integrative and Comparative Biology meeting is held in early January. The deadline for many National Science Foundation pre-proposals is in January. Yes, in theory, people are well organized to have completed all those proposal and presentations and posters before Christmas, but in actuality, for real people, this is a good time to do that work.

And that sort of leads into my biggest point. Is it so bad to like what you do? SciCurious wrote:

Well, I mean...it doesn't help that I...enjoy work. A lot. Part of academic conditioning?

I’m reluctant to admit that I am in the office writing this post, and that I’m happy about working this week. I like the quiet. I like that I don’t have meetings or deadlines. Yet if you’re an academic who likes working more than 40 hours a week, you can be tagged as part of the problem and a victim of mindwashing. For instance:

Nobody dies wishing they published one more paper.

We’re expected to resent work. Mike Rowe talks about this, based in part on his experience on the TV show Dirty Jobs (emphasis added):

We’ve declared war on work, as a society, all of us. It’s a civil war. It’s a cold war, really. We didn’t set out to do it and we didn’t twist our mustache in some Machiavellian way, but we’ve done it. ... We’ve waged this war on Madison Avenue. I mean, so many of the commercials that come out there – in the way of a message, what’s really being said? Your life would be better if you could work a little less, if you didn’t have to work so hard, if you could get home a little earlier, if you could retire a little faster, if you could punch out a little sooner – it’s all in there, over and over, again and again.

A job well done is rewarding. It’s rewarding to be able to look back and see that you have created a body of work. Some people might die wishing they had created more, or done more professionally, or solved an unanswered question. Why should regrets about unfinished things be confined to the personal, non-work realm?

We do have to be careful not to let that desire to work become a macho bullshit test of endurance. In academia, feeling guilt over not working is almost infinitely more common that feeling shame about working when others are not. The expectation that research academics should work long hours, including evenings, weekends, and holidays, is the bigger problem.

But you shouldn’t be made to feel embarrassed if you’re working this week and you’re happy about it. While we’re pushing back against a very real culture of overwork, let’s not forget how great it is to have work that is fulfilling.

Update: I’m tempted to characterize this as another example of work shaming:

Maybe the most relevant answer to academic productivity discussions on Dec 29th is “Nobody cares, go get a life.”

More additional: Post edited for emphasis and clarity, prompted by Julie Brommaert.

Related posts

My new work week
Why cure disease?
Glorifying overworking: another self-inflicted crisis in Science Careers

21 December 2015

Beta testing UTRGV

Grades were due today, marking the official end of UTRGV’s first semester.  How did we do?

Well, we kept the wheels on the bus. The university did not grind to a screeching halt, and students took their classes.

But it’s been a rough semester.

After all the “We are one” pep talks at the start of the semester about the distributed campuses in Edinburg, Brownsville, and so on, I saw a whole lot of people who didn’t get that memo. There didn’t seem to be a lot of work into building bridges between the campuses. Quite the opposite: I saw efforts that seemed designed to insulate people at one campus or another.

When UTRGV was pitched, one of the selling points to the politicians and state administrators would be that UTRGV would be less expensive than UTB and UTPA because the number of administrators would be halved. Instead of a president, provost, and college deans at two universities, there would only be one of each.

Instead of streamlining administration, there are clear signs of huge administrative bloat. While it is true that there is only one dean for each college (for example), what wasn’t factored into the discussion was the rapid proliferation of vice provosts, assistant deans, deputy administrators, and sub-vice deputy positions. So far, I haven’t seen any cases of these administrative positions adding any value to the tasks I need to complete. So far, the only power these individuals seem to have is the power to call meetings.

The first semester was like the beta release of UTRGV. Functional, but buggy and glitchy. I think Beta testing will be continuing for at least one more semester.

Picture from here.

18 December 2015

Today is the day and I just can’t wait!

Today is the day I will finish grading this last assignment I gave my neurobiology students! Just five left! I cannot remember the last time grading has taken so long and taken so much out of me. It’s been tough this semester.

Oh yeah, there’s also a sequel out to a movie that rocked my world some thirty odd years ago.


But apart from this blog post, I am staying off social media for a few days* until I can submit my final grades and avoid all the trolls posting Star Wars spoilers!

* Except maybe Google Plus. Because not much ever happens there, right?

15 December 2015

Tuesday Crustie: Dream house

I’ve shown custom hermit crab shells on the blog before, but artist Aki Inomata has made the more beautiful I've seen.



More here.

Hat tip to Amy Freitang and Liz Neeley.

External links

Why not hand over a shelter to hermit crabs?

14 December 2015

Bad design used to make a good point

Michael Eisen recently took all the journal titles off descriptions of his papers on his lab website. This upset some people, which Eisen chalked it up to “the cult of the journal title.”

Alternate hypothesis: maybe it upset people because it was a bad design decision.

I’ve explored design a lot over at the Better Posters blog, and one of the most powerful lessons I’ve learned has been that good design is about empathy. Good designers empathize with their users, anticipate their needs, and fulfill their needs.

One of the things a person going to a lab publication list wants to do is to be able to find articles that interest them. Removing journal titles makes it harder for users to find articles. And while many (but, importantly, not all) articles have DOIs and links, they are not necessarily things that people relate to as much as a journal title. If you need to scribble a reference on a piece of paper, a journal, volume, and first page number is easier than a DOI link.

The argument that you don’t need journal titles because everything is on the Internet overlooks that the Internet doesn’t need journal articles. People do. People have to work with imperfect memories (some of us more than others) before starting a search on Google Scholar or PubMed. There are many papers that I look at, and I will never commit the DOI or link to memory. I remember the journal that papers were published in quite regularly, though. I don’t remember journals because of their Impact Factors, but because of the content of the journal, the layout and formatting, and other features. A PLOS ONE paper looks different than a PeerJ paper.

By removing a piece of information that users expect and want, Eisen is not meeting the user’s needs. Quite the opposite, he’s explicitly criticizing users who want this information. But good design is not about the designer. It’s about the experience of the end user.

That said, running in the opposite direction is no better:


This was a joke from Yoav Gilad (archived by Claus Wilke; it doesn’t look like that now). But for the sake of argument, let’s analyze it anyway. Here, the changes in text size for the journals (related to Impact Factor) is, for those outside of academia, pointless, and therefore confusing. For those in academia, it looks like an ego trip. (“Oooh, look at the fancy journal I published in!”)

Again: design is not about you.

Now, there is more to life than good design. Removing journal titles from a publication list is a successful act of advocacy against evaluation by “prestige,” which is a much-needed discussion to have. But it may be that users are upset not (only?) because of a cultish belief that journal titles are important signifiers of quality, but because they realize that the design effectively gives them the finger by leaving out something they want.

Update, 15 December 2015: Expanded the post with Gilad’s joke and more discussion.

External links

What’s in a journal name?
Picture from here.

11 December 2015

A strange attack on tenure from Science

Science’s latest editorial is a strange attack on tenure that seems to have originated from some non-academic think-tank rather than anyone associated with academia. But it’s penned by editor Marcia McNutt.

McNutt opens with a strange argument that tenure is preventing women from succeeding in academia.

(Women) are still underrepresented among tenured faculty as compared to, for example, the number of women in similar positions that do not require tenure... A major reason is that young academics must concentrate on their careers to earn tenure at the same time as they would be starting their families, and this issue affects women disproportionately more. ... Whether women see the tenure hurdle and opt out for family instead, or just never opted in to begin with, the result is that there are too few women for a diverse academic enterprise, and if this process does not evolve, how can the highest institutes of learning promote academic freedom and progress?

So let me get this straight. The institution of tenure is the problem for women, and not, say, unrealistic expectations of tenure decision makers, who, by pretty much every set of summary statistics out there, are over-represented by men?

I am willing to bet not one woman working in academic who would feel that their prospects of continued employment would be enhanced by the removal of tenure.

McNutt then argues that, darn it, professors are just old dogs who can’t learn new tricks.

(N)ot all tenured faculty are motivated to stay abreast of new developments. What might have been a booming job market 20 years ago when a faculty member earned tenure may be entirely moribund now. ... Today, tenured professors can continue to hold their positions 40 to 50 years past the date when they received tenure.

Fortunately, I only had to wait a day before this profile of active, engaged researchers who are past traditional retirement age but still doing good science. McNutt’s argument is discriminatory and ageist.

Revising the tenure system to a more flexible form of employment is not going to be easy. ... Those hurt by the system are powerless.

It’s not clear to me who is hurt by the tenure system. I think McNutt is trying to argue that young academics, particularly women, are hurt, because they are more likely to take non-tenured positions. That is not a problem with tenure. This is a problem with adminstrators trying to cut costs.

McNutt’s suggests basically that universities should just give the finger to their tenure faculty and ideals of shared governance.

But it's time for universities to discuss unilateral action and institute some other mechanism.

The editorial comes just a day before this news of faculty – including tenured faculty – being cut from College of Saint Rose. So... yeah. Tenure provides tissue-thin job protection already.

For example, promotion to associate professor could be rewarded with a longer-term contract (10 years), followed by a series of renewable 10-year contracts (or in rare cases, longer contracts) as a full professor. The contracts would be nonbinding, giving the faculty member flexibility to consider opportunities at other institutions.

Oh! How generous! We have to get rid of tenure to make it easier for people to find new work! Because that’s what people want, to have less stability in their lives!

An appeals process (through a national university association) could adjudicate contract disputes or cases of dismissal on grounds of intellectual disagreements.

I’d be more encouraged is I had ever heard of a case of such a mechanism working. In the United States at least, universities are largely under the regulation of the states, so it’s not clear how any national organization could have any teeth.

For goodness’ sake, tenure is not the problem here. The problem is administrators have been cheap, and have tended to exploit their non-tenured faculty with heavy responsibilities and few benefits because they could. Instead of tearing down tenure and turning everyone into contingent faculty and wondering nomads, why can’t we do the opposite?

Why can we not give women on the tenure clock with reasonable performance expectations, not those determined by workaholics with no other responsibilities?

Why can we not provide adjunct and contingent faculty with some of the job security and resources that tenure people enjoy?

Why can we not have strong post-tenure review that ensures that people continue to be competent at their job?

Tenure is not supposed to be a guarantee of a job for life. It’s supposed to provide security against arbitrary dismissal. That long-term security is valuable for research, and I suspect provides a strong incentive for people to work at universities. It certainly did for me.

Pay at universities is often lower than similar positions in the private sector. Would universities who got rid of tenure be willing to bring their pay in line with what people could get in industry? My guess is, “No.”

When McNutt became editor of Science, lots said, “Hey, it’s great to have a woman in charge of Science!” But this editorial is just the latest in a repeated set of regressive articles getting by Science’s editorial team, which have regularly seemed to involve gender issues, and McNutt’s presence as editor doesn’t seem to be slowing things down. I just don’t get it.

Hat tip to Terry McGlynn and Bashir3000.

Additional: In an unrelated but somehow in the same vein of deeply problematic: AAAS, the publisher of Science, elected Patrick Harran a fellow of the society. Harran was charged with four counts of felony following the death of an undergraduate student in a lab accident. More at the Curious Wavefunction and Chemjobber.

Related posts

Breaking brand: Science magazine’s latest self-inflicted crisis

External links

Whither (wither?) tenure?
Saint Rose faculty informed of cuts Friday

“Hey, did anyone win a Nobel?”

Earlier this week, I got one of those emails that had been forwarded through the administrative chain (Provost’s office to dean to associate dean to department chair to faculty).

“Our Strategic Analysis office need to know what awards our faculty have won!”

I keep wondering why individual faculty are being asked to for this information through email when our institution subscribes to a service called Digital Measures that tracks this stuff. Faculty enter their achievements in the system, and people can pull reports from it at any time. I also wonder why this information can’t be pulled from the annual reports faculty have to submit every year.

Although I hadn’t won any awards, I opened up the spreadsheet to see what they were looking for. First line of the spreadsheet:

Nobel prize.

Eyebrow raise.


I keep looking down the list. Pulitzer prize. McArthur award. Awards that get international coverage.

If a faculty member won a Nobel prize, most universities would have press releases sent to every major news outlet and announcements up on their website out before the first morning coffee break.

The thought that adminstration has to ask, “By the way, did anyone on our campus win a Nobel while we weren’t looking?” makes adminstrators look like they’re isolated in some alternate universe bubble that only rarely connects to our own, and they occasionally manage to break through for a brief peek at what’s happening in the reality of faculty, staff, students, and major media outlets.


08 December 2015

Tuesday Crustie: Down deep

This crustacean isn’t big, but space is in short supply when you’re 1.4 kilometers under the surface of the earth.


This little animal may be a copepod - Borgonie and colleagues (2015) list it as Amphiascoides with a question mark behind it, but provide no more details.

This picture has been contrast enhanced from the original in the journal article.

Reference


Borgonie G, Linage-Alvarez B, Ojo AO, Mundle SOC, Freese LB, Van Rooyen C, Kuloyo O, Albertyn J, Pohl C, Cason ED, Vermeulen J, Pienaar C, Litthauer D, Van Niekerk H, Van Eeden J, Sherwood. Lollar B, Onstott TC, Van Heerden E. 2015. Eukaryotic opportunists dominate the deep-subsurface biosphere in South Africa. Nature Communications 6: 8952. http://dx.doi.org/doi:10.1038/ncomms9952

External link 

Animals found living in rock deep, deep underground

02 December 2015

Ideas are cheap

In tooling around Quora, I see a lot of questions from non-scientists that sort of run like this:

“I have an idea! How do I proclaim it to science?”

I’ve heard that authors get similar things all the time. Someone will approach them and say, “I have this great idea for a book. Why don’t I tell you the idea, you write it, and we’ll split the profits?” To which the writer says, “So... you want me to do all the work, and you take half of the money? Thank you, but no.”

To top it off, when people tell the author their brilliant idea for a book, the idea is usually hackneyed and trite. “A man and a woman in a space ship crash land on a deserted alien planet. Their names are.... wait for it... Adam and Eve. Brilliant, huh?”

The cold reality is scientists will probably think your idea is not worthy of their time or talents. Scientists have ideas of their own that they want to test. They don’t lack for ideas.

This is not a knock against non-scientists having ideas. Scientists have much the same reaction to ideas from other scientists. Most of them are not going to influence the research questions that we already want to solve.

Ideas are cheap and plentiful. Testing them is hard.

That’s not to say that scientists don’t need to have ideas. Far from it. One of the reasons why first authorship of papers is so critical for early career scientists is that middle authorship is associated with being a data collector, not the intellectual driver of the project.

To be a scientist, you need ideas plus willingness to put in the grunt work.

External links

The efficient research hypothesis

01 December 2015

Tuesday Crustie: Funding a familiar face


Ah, Emerita analoga. It’s been a while. What have you been up to?

Emerita analoga is one of the sand crabs species I studied for my doctoral work. I found this picture in the usual roundabout way. I was reading an article on science crowdfunding (a topic with which I have substantial experience, though I say it myself) at UT Austin. I went to check out the UT Austin crowdfunding site, Hornraiser, and stumbled across the familiar face above. It’s a project I’m happy to support!

The project is on Emerita analoga’s distribution, which is pretty interesting (shown in green in the map below, from here):


They have these two disconnected places they live: the west coast of North America, from Alaska down to California. They stop through Central America, and pick up again along the coast of Peru and Chile. Are those two different populations connected at all? Are they really the same species, or are they two different species genetically?

I’m happy to support this project! And, of course, you can, too! Because sand crabs are super cute crusties and are awesome!

But where were you when I was doing this kind of crowdfunding stuff years ago, Texas Tribune? Huh?

External links

With Federal Funding Elusive, Professors Crowdfund ResearchAssessing Retention in Sand Crab Populations