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.


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.


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.”


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


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