30 December 2014

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

26 December 2014

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.

23 December 2014

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.

18 December 2014

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

17 December 2014

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!

16 December 2014

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.

12 December 2014

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.

10 December 2014

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.

09 December 2014

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:




05 December 2014

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

03 December 2014

“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.

02 December 2014

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.

01 December 2014

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.

30 November 2014

Science enemies? Franklin and Crick

James Watson wants to sell his Nobel prize because he's all butthurt that he isn't given enough respect.

Any conversation involving Watson – or his late colleague, Francis Crick – invariably leads to a discussion about the role of Rosalind Franklin in cracking the structure of DNA. This go round, Paul Coxon tweeted:

Let's club together to buy Watson's Nobel medal, melt it, and have it recast with Rosalind Franklin's name. Who's in?

The narrative of Franklin's contribution being slighted is very powerful. Many, including family, have guessed about what she would have thought. But as far as I know, Franklin was never interviewed about her reaction to Watson and Crick publishing the DNA structure before her, or using some of her data to work out the structure. She died from cancer before the Nobel prize for DNA structure was awarded, in any case.

Maybe this little incident gives a sense of whether Franklin felt wronged or cheated by Watson and Crick. When she was diagnosed with cancer (which ultimately killed her), she recuperated from her first surgery as a house guest of... none other than Francis Crick.

I've found this anecdote in a couple of biographies (here and here; excerpts below).

It's certainly not definitive proof about what she thought of the whole thing, but it might suggest that Franklin didn't consider her former competitor to be her scientific enemy.


21 November 2014

Saving even the species we hate

Sure, we’ll save this species:


Or this:


But this?


Not only do we not try to save the latter, we’re actively trying to wipe it out.

A recent article notes that one of the effects of breeding endangered species in captivity is that organisms that live on them can suffer. The black footed ferret (top picture) had a louse species specific to it that is probably gone forever. The same holds true for the California condors (second picture from top) bred in captivity, then released into the wild. The captive-bred animals were, perhaps, too healthy... from a certain point of view. Lice that lived on the condor were removed systematically, and as far as we know, that species is now extinct. These do not appear to be the only examples.

Those cases might be unintended consequences. It is possible that the people involved did not know about the parasites that lived on those species, and may have though they were general parasites, rather than ones that specifically lived on those species.

But it raises an interesting ethical issue about how much we value living species.

The third picture in my series is Dracunculus medinensis, also known as the Guinea worm. The Carter Center, founded by former American president Jimmy Carter, is spearheading a campaign to eradicate this species. Admittedly, Guinea worm is a human parasite that has caused a lot of misery to a lot of people over the millennia. Nevertheless, it is as irreplaceable a life form as much as a ferret or a condor. 

I have never heard anyone suggesting that we might want to consider saving this species.

I can see the case for wiping out this species if it was an obligate human parasite, and there was no other way for this thing to live than infect human beings. But Muller (1972) showed decades ago that this species can be reared in captivity, in a non-human host. Some sources suggest it has a fairly wide host range (but haven’t been able to confirm that with peer-reviewed journal article yet).

If you think that conservation of biodiversity is a good thing, should someone start a Guinea worm captive breeding program? The goal might not be to reintroduce the species into the wild, given the harm it causes. Instead, the goal could to preserve it in perpetuity, both for scientific research and because of its intrinsic worth as part of the life on our planet.

Maybe we should have a parasite bank to go next to our seed banks.

Additional: Parasitologist Mark Siddall calls the expected loss of the Guinea worm something to celebrate in this New Yorker article. Mark and I tweeted back and forth on this quite a bit, and I am glad to have his article, with a personal touch, as a counterpoint to my little armchair essay.

References

Jørgensen D. Conservation implications of parasite co-reintroduction. Conservation Biology: in press. http://dx.doi.org/10.1111/cobi.12421

Muller R. 1972. Maintenance of Dracunculus medinensis (L.) in the laboratory and observations on experimental infections. Parasitology 64(1): 107-116. http://dx.doi.org/10.1017/S0031182000044681

External links

Save the parasites!
Conservation biology of parasites (Surprisingly thorough Wikipedia entry)
Carter Center Guinea worm eradication program
Which endangered species would you save?
More harm than good intentions

No wildlife charity campaigns to save parasites. But they should (Added 9 February 2017)

Ferret picture by USFWS Mountain-Prairie on Flickr; condor picture by Pacific Southwest Region on Flickr; both used under a Creative Commons license. Guinea worm picture from Wikipedia.

18 November 2014

Tuesday Crustie: Back of the line!


The segment above (from the BBC series Life Story) shows hermit crabs exchanging shells in a rather remarkable way. I wondered if this had been documented in scientific literature. I’ve read a fair number of papers on hermit crab shell choice, but not this queuing behaviour. And with a little searching in Google Scholar, voila!

Lewis SM, Rotjan RD. 2009. Vacancy chains provide aggregate benefits to Coenobita clypeatus hermit crabs. Ethology 115(4): 356-365. http://dx.doi.org/10.1111/j.1439-0310.2009.01626.x

Rotjan RD, Chabot JR, Lewis SM. 2010. Social context of shell acquisition in Coenobita clypeatus hermit crabs. Behavioral Ecology 21(3): 639-646. http://beheco.oxfordjournals.org/content/21/3/639.abstract

Hat tip to Emily Anthes and io9.

16 November 2014

14 November 2014

“If you’re in your house, why are there elevators there?”


I’m fascinated by how we make and hold beliefs, often in the light on contrary evidence. You see how easy it is for us to have false belief in many patients with brain injury. Many have false beliefs and explain away contradictory evidence effortlessly, which is called confabulation.

This is one of my favourite examples of confabulation, heard by neuroscientist Michael Gazzaniga (from Gazzaniga 2000):

In one patient I had, the patient was a woman who, although she was being examined in my office at New York Hospital, claimed we were in her home in Freeport, Maine. The standard interpretation of this syndrome is that she made a duplicate copy of a place (or person) and insisted that there are two.

This woman was intelligent; before the interview she was biding her time reading the New York Times. I started with the ‘So, where are you?’ question. ‘I am in Freeport, Maine. I know you don’t believe it. Dr Posner told me this morning when he came to see me that I was in Memorial Sloan-Kettering Hospital and that when the residents come on rounds to say that to them. Well, that is fine, but I know I am in my house on Main Street in Freeport, Maine!’ I asked, ‘Well, if you are in Freeport and in your house, how come there are elevators outside the door here?’ The grand lady peered at me and calmly responded,

‘Doctor, do you know how much it cost me to have those put in?

Gazzaniga goes on to explain the reason for this woman’s false belief, due in part to a lesion in her brain:

Because of her lesion the part of the brain that represents locality is overactive and sending out an erroneous message about her location. The interpreter is only as good as the information it receives, and in this instance it is getting a wacky piece of information.

It’s easy to think of this as just an amusing story of someone with brain injury. I think we all have the same mechanisms in our brain that are making sense of the world as best they can. We can all have beliefs that make perfect sense to us, but seem bizarre to outside observers.

Reference

Gazzaniga MS. 2000. Cerebral specialization and interhemispheric communication: Does the corpus callosum enable the human condition? Brain 123(7): 1293-1326. http://dx.doi.org/10.1093/brain/123.7.1293

Photo by Boston Public Library on Flickr; used under a Creative Commons license.

13 November 2014

“Stop flirting, I’ve still got a job to do here,” heard at comet landing

A lot has been written about Matt Taylor’s shirt that he wore during the livestream of the Philae touchdown (links at bottom). I’d like to point out another moment from the P67 comet landing, starting at 6:15:14 in this YouTube video (click text link to go straight to the bit I’m talking about):


The speaker of the moment, Johann-Dietrich Wörner, chairman of the board of the German Aerospace Center (DLR), reveals a P67 polo shirt on stage after the landing.


The presenter, Monika Jones, says, “I want that polo shirt!” Something happens off screen that catches her attention, and she continues, apparently addressing Wörner offscreen, “Not now, we’ve got a few minutes. Change? Stop flirting, I’ve still got a job to do here.”

Now, she said it with a smile, so it’s hard to tell if the presenter was actually offended, or taking it in a spirit of fun. But I had a moment of, “Did she just have to say that?”

Maybe it would have slipped by me if I hadn’t been aware of the shirt issue. But after the shirt issue, and Matt Taylor also talking about Philae coming down for “the kiss,” (also not reported much) I cringed a bit.

Given that I’d seen a bunch of stuff about Matt Taylor’s shirt, I was also saddened when I saw the composition of the audience at the livestream.


I count about five women out of about 35 faces in this one screen grab.When it panned around, the proportion of women in the audience seemed even lower.

Such a stark contrast to the famous pictures of the Indian Mars mission not so long ago:


Update, 14 November 2014: Matt Taylor apologizes for the shirt. This is positive. I do wish he’d also have acknowledged that some of his comments were a bit cringe-worthy, too.


External links

New requirement for scientists: You cannot be a sexist pigdog
Sometimes, a shirt is not just a shirt
Confessions of a teenage dirtbag: Thoughts on shirtstorm
That shirt
Why women in science are annoyed at Rosetta mission scientist's clothing 
Shirtstorm reaction bingo card
Shirts, science communication, and why appearances can be important

11 November 2014

Tuesday Crustie: Sponge-worthy


Periclimenaeus echinimanus is a small sponge-dwelling shrimp from the Red Sea that was only described a few years ago. The species name means “sea urchin hand,” because it has spines on its claws that some of its relatives don’t have.

06 November 2014

Monday morning quarterbacking the UTRGV “Vaquero” decision

The University of Texas System is confirming that the mascot for the University of Texas Rio Grande Valley will be the Vaquero.

I feel sorry for UTRGV president Guy Bailey (third from left; pic from here).

There was just no decision that was going to make people happy. There were a lot of people in Edinburg and McAllen who wanted to keep the University of Texas Pan American’s mascot, Bucky the Bronc. But that choice would have ostracized everyone who had ties to University of Texas at Brownsville.

One of the last surveys showed a lot of people wanted some sort of compromise. That came though in the colour recommendations: UT system orange, plus green from UTPA, plus blue from UTB.

I think Bailey was hoping that “Vaquero” would be that compromise. The word “vaquero” is thought to have morphed into “buckaroo.” Bucky, buckaroo, and there’s a whole horse motif going on... I bet Bailey thought this would be the way to assuage the “Save Bucky” brigade. “There’s still a horse!”

From his opening comments, it was clear that Bailey saw “Vaquero” as Americana that nobody could object to. “Nothing more iconic than a cowboy” is pretty close to what he said in his comments.

While Bailey might have expected that nothing would keep the Bucky fans happy except Bucky, I don’t know if anyone could have anticipated the flames that started pretty much the instant he announced the recommendation.

Having watched this process from the very first meeting at UTPA,“Vaquero” was a name that people suggested. It did not come out of the blue. It was not a random choice from Bailey, or the Board of Regents.

But when it was mentioned as a possibility, I never got, from any of the discussion, a hint of the fury that emerged over the decision. It wasn’t just that people were mad about losing Bucky (which I expected), but the charges erupted almost immediately that the name was racist – and, to a lesser degree, sexist.

I was disappointed to see how fast people trotted out negative Hispanic and Mexican stereotypes on Twitter. Out came the taco and sombrero jokes. I documented a lot of them in my Storify. For me, this was a low point:


Really? I get being upset with the decision. But that? That art’s not okay.

I was also upset by the number of people who said they either would not come to, or wanted to leave, UTRGV because of the mascot. As a faculty member, it bothers me that a foam rubber suit means more to students than the work my colleagues and I do in trying to perform the best possible research and do the best possible jobs of giving students a top notch education.

If the mascot means more to you than the quality of the faculty and staff, I invite you to re-examine your priorities.

I have problems with this choice of mascot. I deeply dislike that it’s “cowboy,” which overlooks that about 60% of UTPA students (and, I’m guessing, UTB students) are female.

There’s already been complaints that people (including Bailey) don’t pronounce it right. Wiki says it’s “baˈkeɾo,” with a B, which makes the connection to “buckaroo” make more sense.

Finally, I think it’s just too obscure a name. I spent years explaining to people where UTPA was. Now I have to look forward to years of explaining what a “Vaquero” is.

It’s interesting to contrast to the decision to name of the institution, where UTRGV bubbled up pretty quickly and had wide community support.

 “Vaqueros” made nobody happy, judging from polls in local media, which show even more rejection of the name than my own. Here’s radio station KURV:


The local newspaper, the McAllen Monitor:


Bailey admitted there was no consensus on the mascot, which must have made his job tough. (Results of one of the last surveys is here. 45% said “none of the above” to the suggested names.) But now, I worry that Guy Bailey has just burned up any support or trust that he might have had from the community.

I wish there had been images like this to go with the announcement. Because, damn, that’s a cool image, and a reminder to me that maybe, just maybe, this name could work.

Update: The UT System has just put out a press release that is, frankly, a little more honest about the pushback than I would have expected.

While the selection drew support from many... it also spurred a backlash on social media, primarily from those who wanted to keep UT Pan American’s nickname, the Broncs.

It then goes on to the “Rah rah rah!” tone more typical of press releases.

Update, 7 November 2014: As I suspected, Bailey argued in the video below that “Vaquero” honors the legacy of the “Bucky” nickname:


External links

Vaquero chosen as UTRGV mascot
The UT-RGV Mascot Saga Ends with The Vaqueros and Apparently Nobody Is Happy 
It’s official: Vaqueros approved as UT-RGV mascot
Opinion: Former school changing mascot, and I’m disgusted

05 November 2014

Watching the UTRGV Vaqueros controversy

Instant controversy: just add Vaquero!

Well, that escalated quickly.

I’m tracking the reaction to the recommendation to have the UTRGV mascot be “Vaquero.” Here’s a Storify:

Bucky is gone - move on!

The mascot of the University of Texas Rio Grande Valley will be the Vaquero (Spanish for cowboy).


The announcement happened just at the start of my General Biology class, so I streamed the announcement, and did a quick poll. The choice got more “Boos!” than anything else.


UTRGV president Guy Bailey noted in his remarks that there was no consensus on the mascot. Judging from my Twitter feed this afternoon, that’s an understatement. I don’t think I have seen a single tweet enthusing over the decision yet. And this was a trending topic on Twitter:


I think Bailey is going to have to do a lot of public relations before people are okay with his decision.

I’ve written about the prospect of “Vaquero” before, and I stand by those comments. In particular, I’m surprised at the choice when another institution, Santa Barbara City College, already has that as its mascot.

I’m even more baffled when I consider the colour choice. The choice of colours was UT system orange (which had to be there) along with UTPA green and UTB blue. As I noted before, one potential mascot that had both those colours: the green jay!

But I am pleased that one way or another, the campaign to #SaveBucky is over. Bucky is going away. Whether you’re pro, con, or indifferent to Vaqueros, let’s move on. It’s a new university with a new identity.

Update: A local television station poll shows little support for Vaqueros.


Related posts

In search of an identity for UTRGV, or: why Bucky must go
The great UTRGV mascot debate continues

External links

UT-RGV mascot recommended to be the Vaquero
UTRGV President recommends “Vaquero” as athletic nickname for new university
UTRGV president recommends "Vaqueros" as school mascot

The man they named my high school after


I went to Matthew Halton High School in Pincher Creek, Alberta. I had never heard the name “Matthew Halton” before attending the school, though while there I learned he was a journalist in World War II. But that was about all I learned.

If I remember right, I even won an award named after Matthew Halton for promise in writing. I took high school awards off my CV years and years ago, so I can’t remember what year I won, or even if I did, for that matter. (Update: My parents confirmed that I did win this award in Grade 12, back in – ugh – 1984!)

For that reason, I was very interested in this interview with David Halton, who carried on his father’s tradition and was a journalist with the CBC. David Halton has just released a book about his father called Dispatches from the Front: The life of Matthew Halton, Canada’s Voice at War.

The interview has got all sorts of great little details, such as that Matthew Halton’s father was the man who cleaned Pincher Creek’s toilets, and Matthew Halton was teased in school as “Shithouse Halton.”

Then there’s the fight between Halton and Ernest Hemingway over Hemingway’s sex scenes...

External links

Matthew Halton audio clips in CBC archives

Picture from here.

04 November 2014

Tuesday Crustie: Democratic choice


Vote!

From here.

Tuesday Crustie: Twentieth anniversary


It’s been almost 20 years since the Fallen Empires expansion of Magic: The Gathering appeared. It included a race of lobster creatures called homarids. Perhaps because the Fallen Empires set was kind of a dud, this article notes:

The naming team felt that Homarids were unpopular enough to warrant a name-change in Alliances, hence “Viscerid.” Their reasoning? “They evolved.”

02 November 2014

Happy birthday, Steve Ditko!

While I was updating the Neuroethology webpage today, I got sucked into watching this excellent retrospective on Steve Ditko, whose birthday is today.

Almost any person claiming to be familiar with comics will recognize Steve Ditko as the original artist of The Amazing Spider-Man. I also knew that Ditko was well known as retiring from the public spotlight. That helps make this documentary completely fascinating, because there is so much about Ditko that just is not widely known. I was particularly fascinated to learn about the character of Mr. A, an Ayn Rand inspired character.

While it seems odd to wish a birthday to someone so famously quiet and retiring (but not retired), I hope Mr. Ditko enjoyed the day.







28 October 2014

Tuesday Crustie: Yeti crab crushes Kremlin!

It’s fair to say I’m a fan of yeti crabs, since I’ve had the yeti crabs on this feature a few times before. (And then there’s the dancing yeti crabs playlist...)

I’m also a big fan of the SyFy series FaceOff, which has its season finale tonight. Last week, make-up artist Cig got into the finals with this kaiju creation:



Cig had never seen a yeti crab before, and decided to make something decidedly more simian than crustacean, keeping in the giant monster tradition started by King Kong.



While I did enjoy Cig’s take on the yeti crab, I have to confess that I am pulling for Dina tonight! She captured my attention with this creation on episode 1 of this season.


And she’s held it ever since. I particularly loved her aquatic Aphrodite (middle row, third from left):


22 October 2014

Should you reply to spamming students?

A colleague, who is a new assistant professor, asked on Facebook, if he should reply to an “endless” stream of emails from international students.

I know the kinds of letters this person is asking about. Many show the candidate has extremely limited ability to express him or herself in written English, the tone is often obsequious, and the letters are often clearly “form” letters sent to who knows how many institutions.

What’s the right course of action? On the one hand, there is an actual person on the other end. A person who has probably gotten bad advice, but still. On the other hand, it can take up a huge block of time to reply to all of these.

If someone sends you a cut and paste inquiry, it’s okay a cut and paste response. Signs of a cut and paste from a student include the opening, “Dear Sir / Madame,” or discussing research interests that are nowhere near the kind of stuff you do.

Only if someone has clearly written a personalized inquiry to you, that shows they understand what you do, should you spend the time to write a personal response.

I don’t have an endless stream of these letters - and I am the grad program coordinator - so I do reply. I send links to our entry requirements and program FAQ, and answer any direct questions in the letter.