Category Archives: science

academia, Ronin Institute, science

The Case for Independent Scholarship #3: On Workaholic Scientists

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So, Sam Arbesman has a post up at Wired where he discusses a recent study on the work habits of  scientists in around the world. As a proxy for “working,” the authors look at the pattern of downloads of papers or book chapters from Springer. The work makes use of a cool real-time mapping of IP addresses accessing those papers. If you want to see what it looks like, check it out here: http://realtime.springer.com/map.

They do a more detailed analysis of the top three countries (in terms of total number of downloads in about a week’s worth of data), the US, Germany, and China. Correcting for time zone differences, they find these patterns:

On the left side, each line corresponds to a different day, with the more solid lines being weekends, and the thinner ones being weekdays. On the right, the weekends and weekdays are averaged.
A couple of things that will probably come as no surprise to most of the academics out there. 
(1) the daily hump starts picking up around 9 or 10 in the morning, and carries on until nine or ten at night.
(2) the weekday hump is bigger during traditional “working hours”, but evening work hours are pretty consistent throughout the week.
Interesting cultural differences pop out that might not be as predictable. It looks like China has longer and/or more simultaneous breaks for lunch and dinner. (Although, given the common practice, at least in the US, of eating lunch at your computer, maybe the lack of those dips in the top panel are somewhat predictable.) Americans seem to be working a lot more in the middle of the night compared with their German and Chinese counterparts, while the Chinese seem to show less of a difference between weekday and weekend work habits.
The authors’ conclusion, and one that is echoed in Sam Arbesman’s commentary, is that this work pattern is consistent with what most academic scientists would probably tell you. Academia is a full-time job. And not a full-time job in the sense of a forty-hour work week, but a full time job as in, you sleep, eat, and work.
So is that a good thing or a bad thing? Well, on the one hand, you’ve got all of these highly trained, highly educated people working really hard and getting paid not a whole awful lot on a per-hour basis. Good deal, right?
On the other hand, it leads to a really crappy lifestyle, where the long hours come at the expense of time spent with family, hobbies, or even taking an interest in subjects outside of the very narrow range defined by your research. If you care about a broader definition of human happiness,  one that treats people as an end rather than a means, this is not a great way to structure your industry. 
Beyond that, it is important to remember that science, like all academic fields, is a fundamentally creative enterprise, and working longer hours does not necessarily translate into better results. Creativity has to be fueled by experience, and a broader range of experience can lead to asking more interesting questions and coming up with more original answers to those questions. The pressures that lead people to download papers from Springer from morning till night don’t necessarily lead to the best science.
I should note that Sam’s coverage also includes a plug for the Ronin Institute, because Sam is a freakin’ rock star!

Wang, X. W., Xu, S. M., Peng, L., Wang, Z., Wang, C. L., Zhang, C. B., & Wang, X. B. (2102). Exploring Scientists’ Working Timetable: Do Scientists Often Work Overtime? Journal of Informetrics, 6 (4), 655-660 DOI: 10.1016/j.joi.2012.07.003

Behavior, biology, comic, Darwin Eats Cake, evolution, science

The selfish herd

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So, one of the most interesting questions in evolutionary biology is the origin of collective behaviors. This can be the complex division of labor that we see in social insects and human societies, flocking behavior in migratory birds, or microbial formation of biofilms. It can be predators engaging in collective hunting, or prey engaging in collective being hunted. It’s this last one that we’re going to be talking about today.

As with many questions in evolutionary biology, there are a couple of dimensions that people are interested in untangling: proximal and ultimate causation. Proximal explanations focus on the “how” part of the solution, as in, “what are the molecular, genetic, etc. mechanisms and environmental cues that result in this behavior?” Ultimate explanations focus on “why,” in the evolutionary sense of “what were the selective pressures that led to the evolution of this behavior?”

Herding or flocking behavior is a classic case. For example, why do sheep hang out in a big group, in contrast to say, leopards, which tend to be pretty solitary? There are a number of possible (and not mutually exclusive) ultimate explanations, but the most talked about one is probably defense against predators.

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Back in the mid-twentieth century, it was common for biologists to talk in fairly loose terms about collective behaviors having evolved as a result of their benefits to the group. Then, in 1966, G. C. Williams published Adaptation and Natural Selection, which dropped a lot of truth into the community. In particular, it emphasized the gene-centered view of natural selection that hit the public consciousness with Richard Dawkins’s 1976 book, The Selfish Gene, and which has remained the dominant paradigm in evolutionary biology ever since.

Williams demonstrated that group selection, while possible, will generally be a much weaker force than selection acting on the individual. Therefore, it is good practice to look for evolutionary explanations at this lower level. Given plausible adaptive stories at the individual and group levels, one should favor the individual-level story. While the two stories might not be mutually exclusive, individual-level selective pressures are more likely to have played an important role in  the evolution of any particular trait than group-level selective pressures (all else being equal, of course).

In 1971, W. D. Hamilton published a theoretical analysis that brought this individual-level perspective to herding behavior. Hamilton argued that all you need is for animals to be trying to evade predators as individuals. If there are other individuals of their type around, they just need to try to position themselves between other individuals. Here’s how Hamilton draws it:

This frog wants to position itself between the two frogs on the right. That way, when the sea snake comes up, it will eat one of the frogs at the edge, and the one in the middle will be safe.

All you need is for everyone to follow one simple rule: when a predator comes, position yourself between two other individuals. What you get then is a tight cluster of individuals.

You can actually try this at home. You probably need about eight or ten people. So, most of you might not be able to try this at home, but you could maybe try it at school or work. Have each person pick two other people in the group (but don’t tell who your picks are). Then, everyone tries to get between the two people they picked. What you’ll get is something a lot like a cluster of frogs climbing all over each other to get away from a sea snake.

Frogs maneuvering to get between other frogs results in the formation of a clusterf**k of frogs. I know, right? I was surprised, too, but my herpetologist friends assure me that “clusterf**k” is the official collective noun for a group of frogs. Don’t even ask about sea snakes. You don’t want to know.

Bonus activity: after you’ve disentangled yourselves from the frogpile, try this one. Each person picks two people again, labeling them “A” and “B” (in your head). Again, no one needs to say whom they picked. Now, each person should position themselves so that their “A” person is between them and their “B” person. If it helps, imagine that “A” is Mitt Romney, that “B” is the American People, and you are Mitt’s tax returns. Your job is to position yourself so that Mitt keeps the American People from seeing you. I won’t spoil how it comes out.

So, Hamilton’s model provides a nice, simple model that can produce the observed behavior. The model is attractive because (1) it requires selection only at the level of the individual, and (2) it requires each individual only to follow a very simple behavioral rule. The collective behavior is an emergent property requiring no coordination at the group level.

Now, there’s a new paper out that is attempting to look at this empirically, in sheep. The study involves strapping adorable GPS backpacks on a bunch of sheep (Figure 1c, below) and then letting a sheepdog chase them around.

You can look at the movies here. It’s only a brief communication, and does not really nail anything down, but the authors interpret their results as broadly consistent with the selfish herd model. In particular, they are able to see that individual sheep seem to be trying to get to the center of the flock.

The cool thing is more the potential for this type of experiment. Yes, Hamilton’s model is attractive and parsimonious, but if we want to understand the rules that actually govern the behavior of sheep when they are faced with a predator (or, in this case, an annoyator), we will need to get good quantitative data on individual behaviors in a variety of contexts.

Plus, look at that little GPS backpack!

I’ll leave you with this.

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King AJ, Wilson AM, Wilshin SD, Lowe J, Haddadi H, Hailes S, & Morton AJ (2012). Selfish-herd behaviour of sheep under threat. Current biology : CB, 22 (14) PMID: 22835787

Hamilton, W. D. (1971). Geometry for the Selfish Herd Journal of Theoretical Biology, 31, 295-311 DOI: 10.1016/0022-5193(71)90189-5

science

Copper nanotubes and acronym hilarity

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So, I just learned about this paper via the Twitter. It’s a short piece in the journal Chemical Communications entitled “Electrochemical synthesis of metal and semimetal nanotube–nanowire
heterojunctions and their electronic transport properties.” Nothing to see here, right? Well, the repeated references to copper nanotubes lead to fifty uses of the acronym “CuNT” in the three-page paper.

The paper is by a group of researchers in China, and I can’t quite decide if the lesson here is to run your acronyms past colleagues who are native speakers of various other languages, or if the lesson is to absolutely never do that, lest you should deprive the world of gems like this.

If you’re sufficiently juvenile that you’re still laughing about the copper nanotubes, the School of Chemistry at the University of Bristol has multiple web pages dedicated to molecules with names like “arsole,” “cummingtonite,” and “moronic acid.” Check it out.

via Colin Stewart via Ed Yong.

biology, evolution, population genetics, science

Blue-eyed-people-are-all-related zombie news

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So, you know how sometimes at night you’re lying in bed when you burp, but then the burp turns out to actually be you throwing up into your mouth just a little bit, and it tastes like a combination of whatever you ate for dinner and evil? Well, this is sort of like that.

Four years ago, a group of researchers from the University of Copenhagen published a nice paper on the genetics of blue eye color. In that paper they look at a bunch of Danish families in which some people have blue eyes and some have brown eyes (or, combination blue-brown eyes, which, for purposes of this study, are treated as non-blue). They also look at a small sample of non-Danish blue-eyed folks: five from Turkey and two from Jordan.

The paper makes a compelling case that the pure blue eyes phenotype depends on a particular nucleotide substitution that alters regulation of the gene OCA2. Furthermore, there is an extended haplotype around the key mutation that is shared by everyone in their sample (a few people have additional nucleotide substitutions that most likely post-date the key functional mutation). This suggests that, while there are many genes that contribute to eye color variation and to pigmentation in general, there may be a single critical mutation responsible for all of the blue eyes out there. Which is pretty cool.

For reasons that I still don’t understand, this study has popped back into the news recently. In particular, an article that looks to have been written back in 2008 in USA Today was “updated” in February, and has resurfaced on AOL, which describes it as a “study from USA Today,” and warns people with blue eyes about the dangers of falling in love with another blue-eyed beauty. Presumably because of incest (also shown is a clip from HLN — the artist formerly known as CNN Headline News — featuring the anchor doing a whole “ick” thing).

In worst-of-media-coverage-of-science fashion the reports that I have found (both from 2008 and from 2012), coverage focuses on stuff from the paper that is tangential, irrelevant, or wrong.

First, “all blue-eyed people are related.” Where to start. The researchers suggest that the mutation might have arisen 6000-10000 years ago in the Black Sea region, prior to the Neolithic agricultural expansion into Europe. If we assume a generation time of, say, 25 years, that is 240-400 generations. If we look back that far in the past, even just to the 6000 year mark, each of us has 2^240 ancestors. That’s 1.7 x 10^72, which, you will notice, is not just much larger than 7 x 10^9 (the current population of the whole world), but is close to the ballpark of the total number of atoms in the universe.

The fact is, once you go back more than a few hundred years, each of us has a list of ancestors that features the same people over and over again. Not only are we all related, we are all related over and over and over again. While your brother may not be your cousin, your tenth cousin is quite likely to be your seventh cousin as well.

So, yes, all blue-eyed people are related, but there is not really anything here to suggest that they are significantly more closely related than any two people.

Second, both the 6000-10000 year timeframe and the Black Sea origin of the mutation — both of which featured heavily in press coverage of the paper — are completely unsupported by anything in the data. What the authors actually say is this:

The mutations responsible for the blue eye color most likely originate from the neareast area or northwest part of the Black Sea region, where the great agriculture migration to the northern part of Europe took place in the Neolithic periods about 6–10,000 years ago (Cavalli-Sforza et al.1994).

The high frequency of blue-eyed individuals in the Scandinavia and Baltic areas indicates a positive selection for this phenotype (Cavalli-Sforza et al. 1994; Myant et al. 1997). Several theories has been suggested to explain the evolutionary selection for pigmentation traits which include UV expositor causing skin cancer, vitamin D deficiency, and also sexual selection has been mentioned. Natural selection as suggested here makes it difficult to calculate the age of the mutation.

That is, we don’t know how old the mutation is, and have not tried to perform any sort of analysis to ask the question. That’s fine, because what the paper actually does is provide us with a basis for asking these sorts of questions, although that will require more extensive sampling.

The supposition here is based solely on the fact that there was this expansion of agriculture (along with, to a not-fully-characterized extent, an expansion of the genes of the people who developed that early agricultural technology), and that stuff in Europe probably came with that.

The actual way to ask the question would be to go and sequence the DNA of a bunch of folks from all across Europe. To first approximation, we might assume that the mutation first arose in the region where the blue-eyes haplotype shows the greatest within-haplotype genetic diversity. For example, if the mutation first arose near the Black Sea, we should see more genetic variation right around the key mutation among blue-eyed people near the Black Sea. If the allele arrived more recently in Sweden, blue-eyed Swedes would be more genetically similar to each other in the same genomic region, simply because there would have been less time for differences to accumulate.

All else being equal, we might expect the geographical origin of a particular mutation to be at the central point of its range, or near the place where the mutation has reached its highest frequency. That supposition would place the origin somewhere near the Baltic (rather than the Black) Sea. But, there is good reason to believe that this mutation may have been subject to selection. The blue-eyes allele also affects other aspects of pigmentation, and lighter coloring is thought to have been favored at higher latitudes due to the reduced incidence of sunlight.

The fact that we think that natural selection would have pushed the mutation northward means that that its origin was probably somewhere to the South of its current center. Exactly how far depends on a bunch of details, like the strength of selection, and how that strength of selection changes as you move from South to North.

The problem is that, to do it right, you would have to build a model that explicitly incorporates the agricultural expansion and natural selection acting on OCA2, with the strength of selection favoring lighter pigmentation depending on latitude. Maybe also the fact that there are other genes affecting pigmentation. It is something that is doable, especially now that we have a specific gene to focus on, but at this point what we have is a bunch of speculation.

So, to recap, 1) Cool paper. 2) Sex between blue-eyed people is not incest. 3) We have no idea when or where this mutation came from, but it is now conceivable that we could ask the question. 4) Embarrassingly bad science reporting spontaneously rises from the grave four years later and tries to eat your brain.

Eiberg, H., Troelsen, J., Nielsen, M., Mikkelsen, A., Mengel-From, J., Kjaer, K., & Hansen, L. (2008). Blue eye color in humans may be caused by a perfectly associated founder mutation in a regulatory element located within the HERC2 gene inhibiting OCA2 expression Human Genetics, 123 (2), 177-187 DOI: 10.1007/s00439-007-0460-x

biology, music, science, video

Ph. Diva and the Mystery Band

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So, there are a LOT of lab-life-themed music videos out there. Mostly, they are amateur things put together by groups of under-worked grad students, where they change the lyrics to some popular song, or “pop” song, as the kids say.

This is a whole different thing, with significant production value, which is what happens when a biotech company gets in the game.

It lacks some of the charm and energy of dorky grad students singing Lady Gaga off key. On the other hand, it lacks all of the dorky-grad-students-singing-Lady-Gaga-off-key-ness of dorky grad students singing Lady Gaga off key.

This is actually the second video in a series. The next two will be out later in the year. You can see the prequel here.

Behavior, biology, comic, Darwin Eats Cake, evolution, evolutionary psychology, psychology, religion, science, sex

Toxoplasmosis Extravaganza: Ride Complete!

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So, this week at Darwin Eats Cake, we celebrated our one-year anniversary with a series of nine strips on the zooparasite Toxoplasma gondii. This parasite, which causes Toxoplasmosis, is the reason why pregnant women are encouraged to avoid cat litter.

Here’s the full series, presented for your one-stop-shopping viewing pleasure. The strips do not, I think, assume any expert biological knowledge, so you don’t need to be a parasitologist to enjoy them. However, a dorky and juvenile sense of humor will help a lot. Alternatively, you can read them on the Darwin Eats Cake website, where they look a little better, I think. The series starts at http://www.darwineatscake.com/?id=101.

At this point, Darwin Eats Cake will return to its regular programming schedule, with twice-a-week updates, usually on Mondays and Thursdays, except for those days that have been recognized as official holidays by the Darwin Eats Cake Council of Freeholders and its chairwoman, the duly elected Queen of Naboo.

So, stop by on Monday for a new strip, or any time to trawl the archive: http://www.darwineatscake.com.





Behavior, biology, comic, Darwin Eats Cake, evolution, evolutionary psychology, neuroscience, psychology, religion, science

It’s Toxoplasmosis week at Darwin Eats Cake

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So, tomorrow (March 13) marks the one-year anniversary of the launch of my webcomic Darwin Eats Cake on its very own website (here). Normally, Darwin Eats Cake updates approximately twice a week (hemicircaseptanally), on approximately Monday and Thursday (circa-Mondarily and circa-Thursdarily, I assume). However, to mark this special anniversary occasion, we are rolling out a daily series of strips on Toxoplasma gondii, the parasite responsible for Toxoplasmosis. This bug was recently in the news thanks to a profile of Jaroslav Flegr published recently in the Atlantic (here).

Here are the first two of this week’s six strips:

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music, religion, science, sex, video

The most astounding thing about the universe

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So, Neil deGrasse Tyson is awesome, with a capital AWE. Here’s one reason why. This is a video of Tyson describing the single most astounding fact about the universe. His answer is from a 2008 interview, which has recently been set to music and accompanied by an excellent video by Max Schlickenmeyer.

via io9.

Of course, the other thing that I love so much about him is the way that when you look at him, his eyes are like “I would like to make sweet, sweet love to you,” but then his clothes are all, “but I am physically incapable of doing so.”

Just look:

I mean, seriously, how can you not love this guy?