A Washington Post article from the weekend looks at current job prospects for scientists. It ain’t pretty in the United States. Ends with this quote:
Haas, the former drug company chemist, has even harsher words. She plans to “get out of Jersey and get out of science” when her daughter graduates from high school in two years. “She’s very good at everything, very smart,” Haas said of her daughter. “She loves chemistry, loves math. I tell her, ‘Don’t go into science.’ I’ve made that very clear to her.”
And that’s the sort of reaction that parents reserved for when their kids said they were going to try to become artists or actors: “You’ll never get a job doing that!”
The good news is that admonitions from parents are only occasionally effective. And people do get jobs doing “that.”
I am thoughtful about what career advice I should give, however. Our institution puts a lot of effort into encouraging scientific careers. We have undergraduate research programs, funded by HHMI and NSF (thanks, guys!). We have high school internships. We have HESTEC, with tons of events aimed at even younger kids. (Our mission is different from other universities, though. We have many Hispanic students. Part of these program are tied to efforts to increase representation of Hispanics in science.)
Obviously, I owe it to students to let them know what the real deal is about this career. Should I actively discourage them from pursuing a scientific career?
I don’t think so, mainly because of the stage our students are at. We don’t have Ph.D. students. In theory, we could have post-docs, but nobody does. We have undergraduates and some master’s students.
A student graduating from our program who wanted to become a full-fledged lead scientist with a doctorate is probably ten years away from completing their training. Six years for a doctoral degree, four years for post-docs.
A lot can happen in ten years.
Admittedly, the long terms trends are not good. But trends can reverse sometimes.
It is important that people considering science understand how far off their goal is. They need to weigh the prospect of that long training period versus doing things right after finishing their bachelor’s degree.
I would still encourage students to consider science as a career, with the caveat that they not commit the Concorde fallacy. Make sure you have a getaway plan going in.
That’s right: fossils from the Carboniferous and Permian times had insects with single wing lengths of more than 30 cm (that’s a foot for those of you still using Imperial measurements).
One hypothesis for why insects were able to be much bigger was that there was more oxygen in the atmosphere then. A new paper by Clapham and Karr suggests that’s true... up to a point.
Looking at the fossil record and that for oxygen, they find a good correlation between oxygen levels and insect sizes up until the end of the Jurassic. After that... the correlation falls apart. During the Cretaceous, the oxygen levels go up (though not as high as the Permian or Carboniferous), but the insects get smaller. And insects get even smaller after the K-T boundary, even though oxygen is pretty stable.
Clapham and Karr suggest that flying predators, notably birds, play a role in the reduction of insect body size. This struck me as counterintuitive at first, as larger bodies are explained as possible defences against predation. Clapham and Karr’s idea is the battle in the air is over manoeuvrability. Big animals can’t twist and turn and dodge so easily. Perhaps with the reduced oxygen levels of the Cretaceous, insect physiology wouldn’t support the re-evolution of large bodies as a defence against bird predators.
If you like your insects small, thank a bird.
Reference
Clapham ME, Karr JA. 2012. Environmental and biotic controls on the evolutionary history of insect body size. Proceedings of the National Academy of Sciences 109(27): 10927-10930. DOI: 10.1073/pnas.1204026109
The great thing about this picture of CNN’s coverage about the announcement of finding the Higgs boson (spotted by Jon Mitchell)...
Is how wonderfully multi-purpose it is. I can use it as a slide in my next talk, no matter what the subject is!
Yesterday’s announcement that the teams at the Large Hadron Collider had almost certainly found the Higgs boson once again focused my attention on how different the community standards of scientists are. Karen James asked:
How is the Higgs announcement today anything other than science by press release?
This led to some conversation on Twitter with Karen, Ed Yong, Matthew Francis, and Cathy Kerr (mainly - apologies if I have overlooked others!) about why the physics community is perfectly cool with this. In biology, you’d probably get smacked down pretty hard for having a press conference without a paper at least accepted to show for it.
Twitter may not have been the best forum for this discussion. I referred to the Higgs announcement as a “shortcut” – not a good term in retrospect – which Ed rightfullycalled me on. Different community standards.
What I was fumbling to say was that in science, we do try to standardize our approaches to things to a fairly large degree. We deal in evidence. We subject ideas to peer review. Papers are the major coin of the realm. Credit is usually given to the person who makes the first announcement. It’s not absolutely uniform, but in broad strokes, people in one field of science can recognize the processes in other fields of science.
Why is there so much divergence in how results are communicated? Would there perhaps be some benefit in trying to harmonize how scientific results are communicated? We could, dare I say it, become a little more empirical about this. What are we out to achieve with announcing scientific results, and are some ways better to do this than others?
Comic Sans
The announcement may have also moved the awareness about Comic Sans and its use in the scientific community to a new level. That the cane toad of type appeared in the Higgs presentation itself became a newsworthystory for the media.
Some thought this was a deliberate move to provoke people. Some thought they were using it ironically to show they have a sense of humour. Some thought that making a big scientific discovery like this granted you immunity from prosecution for all past, current, and future type crimes. Me? I’ve made my views known before.
You can do better than that, physicists.
Higgs humour
All that aside, I had fun on Twitter putting standard anti-science arguments with this discovery, with the #HiggsDenier hashtag:
"Those graphs are perfect. A little TOO perfect, if you ask me!" #HiggsDenier
"Physcists getting rich off the government grants to find a particle HAVE to say there's a boson or lose their funding." #HiggsDenier
"They're announcing the discovery by a press conference because they know the results can't pass peer review!" #HiggsDenier
"Genesis doesn't say, 'In the beginning, God created a 126 GeV boson.'" #HiggsDenier
"Discovery of Higgs boson, particle physics 'missing link', just creates two new gaps in the standard model." #HiggsDenier
"A 126 GeV particle a perfectly consistent with my theory that the universe is made from earth, air, fire, and water." #HiggsDenier
"They want to teach the Higgs boson in school? What about parental authority? I should be able to decide what my kids learn!" #HiggsDenier
"What if the Higgs boson falls into the wrong hands? It could be the engine for new weapons of MASS destruction!" #HiggsDenier
I’m indebted to Nina Simon for bringing this story to my attention: Belgian monks who brew beer. Nina summarizes the story thus (my emphasis):
Westvleteren 12... is produced by the monks of the Abbey of Saint Sixtus of Westvleteren in Flanders, Belgium. You can only reserve a bottle by phone. You must pick it up in person at the Abbey at a specific time on a specific date. You can only buy a small amount, and you are limited to one purchase every 60 days.
The episode is mostly focused on the thrill of the hunt, and all the attendant ways exclusivity fuels desire. But late in the episode (minute 9), when the supplicant finally drinks the beer at the monastery, he is underwhelmed. The beer is terrific, but the experience is unfulfilling. He feels anonymous. He feels disconnected. He made it to Mecca, and it’s kind of eh.
Why the disconnect? As Roman Mars, the show’s host, puts it, “You, the consumers of beer, are not the real customer. God is.” The monks make beer to support their monastic lifestyle, not to serve consumers. The exclusivity and the complicated path to purchasing the beer are not branding strategies to trump up the value of the beer. They are limitations that enable monks to spend most of their time being monks.
It seemed to me that this story is a great metaphor for a lot that we complain about regarding academic science.
(No, I don’t want to suggest scientists, like monks, can / should sacrifice everything for a “higher purpose.” I think that’s a horrible thing for a profession, not something that should be celebrated.)
Take science outreach, which is a constant source of “We should do better!” Or undergraduate teaching. It’s possible that the results here are sub-optimal because the system is not primarily concerned with those outcomes. The system tries to enable scientists to do science. So you get a sub-optimal system, much like the monk’s sales system is sub-optimal.
In memory of Andy Griffith, who died today, my favourite show of his, by a long ways.
I always loved hoe the narrator in the opening hit, “...and they went to the moon.” It hit just the right note of admiration and awe about the achivement.
I liked this show a lot when I was a kid; had a poster of the spaceship up on my wall, from this:
It’s interesting to look back at the show now that we are just starting to see private space flight.
This is Euastacus bindal. It does not have a common name, because it is not common. It is the exact opposite of common. It is astonishingly rare.
Before the new paper by Furse and colleagues, there were a grand total of three specimens that had been seen to science. This picture is the first time the colour of the live animal has been shown to the scientific world.
Furst and collegues went back to the location where other specimens were found, on a mountain in Queensland, Australia. They found that this crayfish confined to about one square kilometre. That’s it. That’s smaller than the campus of the university where I teach and work.
Their investigations of the animal’s ecology is that it needs cool rainforest habitat, and that’s only found at the very top of this mountain. The nearest similar habitat is a couple of hundred kilometers away.
From a conservation viewpoint, there is some good news, though. That entire kilometre is within a national park. Pressures like urban development or exploitation might not be threaten this species.
Reference
Furse JM, Bone JWP, Appleton SD, Leland JC, Coughran J. 2012. Conservation of imperiled crayfish — Euastacus bindal (Decapoda: Parastacidae), a highland crayfish from Far North Queensland, Australia. Journal of Crustacean Biology 32(4): 677-683. DOI: 10.1163/193724012X633405
Why build a nest if you’re a fish? A bird’s nest can be up in a tree to keep away from predators, but a fish nest is, well, in the water. Siamese fighting fish (Betta splendans) are one of several aquarium fish that are bubble nest-builders. The male builds the nest and cares for the eggs after laying. Indeed, the male drives the female away from the nest.
One of the problems with putting all your little developing embryos or babies in a confined space like a nest is that if an infection hits, it might hit all of them. Betta nests without males are often hit by water molds (the same obscure group of organisms that also cause crayfish plague). Lots of other animals have some element of their nest that act as antimicrobials, and Brown and Clotfelter hypothesized this might also be true for the fighting fish.
Reasonable idea, but wrong.
They tested bubble nest material against two bacteria and a water mold. There was no evidence any of the bacteria were held back or inhibited by the nest material compared to a control.
Surprisingly, the presence of the nest material, made things worse With the water mold! More eggs were infected faster in the presence of bubble nest material than in plain water. Nests seem to be a horrible idea!
But wait! Brown and Clotfelter suggest that nests have an important function. Siamese fighting fish are popular in aquariums precisely because they are used to living in very low quality water, with little oxygen. The nests may be necessary to keep enough oxygen to the eggs for them to develop. And, because so few other animals can live in the same waters as Siamese fighting fish, the risk of predation may not be very high.
It might explains why you have parental care by these fish: this may be the one thing keeping those eggs viable and parasite free.
It’s nice to see that there are still interesting research projects that can be done even with these common aquarium pets.
Reference
Brown AV, Clotfelter ED. 2012. Fighting fish (Betta splendens) bubble nests do not inhibit microbial growth Journal of Experimental Zoology A: in press. DOI: 10.1002/jez.1740
Photo by christyfrink on Flickr; used under a Creative Commons license
An forthchoming paper by Brucker and Bordenstein (B&B) argues that bacteria living inside larger eukaryotic organisms – the ones we can see think and think of as “real” organisms – could be having major impacts of their evolution.
Specifically, bacteria could be causing these larger organisms to speciate.
This sounded strange at first, but then I thought about the ever increasing attention to, and understanding of, the “microbiome.” Go back a few years, and you wouldn’t hear the statistic, “There are more bacterial cells in your body than human cells.” This is now common knowledge, at least among the science savvy crowd.
Brucker and Bordenstein point out that bacteria are ubiquitous, specific to particular host species, and drive changes in genes associated with immunity. We’re hearing more about treatments that pay attention to the microbial communities within us, partly because we’re finding out that disturbances in gut microbes could be related to all kinds of medical issues. And some people have been successfully cured by fecal transplants – which has a certain shock value.
The importance of the microbiome lends some plausibility to the claim that bacteria could affect speciation.
First, Brucker and Bordenstein argue that bacteria can create reproductive barriers that span multiple generations. Their main example is an experiment involving Wolbachia (pictured) infecting Drosophila. Wolbachia do all sorts of strange things to the hosts they affect, largely in messing up sex ratios of offspring and more. While interesting, I think it’s fair to say that Wolbachia are unusual in their interaction with their hosts. They also note, however, that bacteria are involved in generating cues important to mating, like odours. There are also cases of bacteria that can induce parthenogenetic reproduction. Again, Wolbachia is one, but it’s not the only one.
Having established the possibility that bacteria could split populations into species before mating, Brucker and Bordenstein turn their attention to how bacteria could exert selective pressure after mating.
One extremely interesting theoretical point is that symbiotic bacteria be more efficient at causing hybrid incompatibility than genes. Imagine that there are three genes (version 1: X, Y, Z, version 2: x, y, z,) in different species, and some versions of those genes are not compatible. If a hybrid gets X and Y, the hybrid dies. With three such genes, there are three possible “bad” combinations. But if there is X, Y, and a bacteria (B), there are six possible “bad” combinations, so you get stronger selection pressure against hybridization. There seem to be no “real world” examples of this, though.
Brucker and Bordenstein also note that if hybrids have defective immune systems, they will be more prone both to infections and autoimmune disorders, and these will also provide additional selection pressure against hybrids. While true, these don’t seem to be selection pressures that are specific to bacterial symbionts, which is ostensibly what the paper is about.
Could bacteria be secretly driving evolution under our noses? Hard to say now. Many of the examples here are either theoretical, or are drawn from fairly specific examples, like Wolbachia. Speciation being driven by bacteria endosymbionts or microbiomes may be happening at very low rates, or may be even be only a theoretical possibility.
But I certainly don’t want to underestimate the possibility, or the power of bacteria.
“This is the Age of Bacteria,” Stephen Jay Gould used to say. “It’s always been the Age of Bacteria.”
References
Brucker RM, Bordenstein SR. 2012. Speciation by symbiosis. Trends in Ecology and Evolution: In press. DOI: 10.1016/j.tree.2012.03.011
I didn’t want to write it – not because I was coerced, or because I don’t think it’s valuable – but because I would rather have had one paper rather than two.
Early in 2011, I co-authored a modeling paper on Marmorkrebs with my colleague down the hall, Paty Feria. We had tried to figure out the risk of Marmorkrebs invading in places where they had been documented as being released, or were available in the pet trade. Despite rumours, there was nothing confirmed about Marmorkrebs in any location in Asia at the time.
But papers take time to write. The manuscript was already done and had been submitted to journals by late summer 2010.
In early fall 2010 that I’d learned of an older report of Marmorkrebs being found in Japan at the Sapporo Salmon Museum (pictured above) in 2006. It had been reported in a book, and one written in Japanese, so it not the easiest piece of information to come across using my usual Internet search strategies. I dutifully reported on the Marmorkrebs blog.
We thought out paper was based on a complete set of records of where Marmorkrebs had been found... and then we discover, not just another record, but one in a whole new continent. This fact was probably influencing my SciAM Guest Blog post (later included in Open Lab):
Scientists like to think of themselves as being ahead of the curve. In the case of Marmorkrebs, we’ve consistently been about a few years behind events on the ground. Pet owners in Germany report the crayfish to scientists — paper comes out three years later. Marmorkrebs show up in market in Madagascar — paper comes out four years later. This isn’t anyone’s fault; it’s an indication both of how long careful science takes and how rapidly events are unfolding.
If anything, though, finding of the Marmorkrebs in Japan probably pushed us to get the first paper out, feeling that it could be useful in helping policy and planners.
That left us with a new paper to write. We had one individual Marmorkrebs in the Japanese ecosystem, so the threat was real. There were interesting conservation and economic impact angles here, too.
We did end up pushing things further in this paper in terms of the models, and gained a new collaborator in the process. Based on some of the feedback we got, we did not just run the same models as in the 2011 paper. Now, there are five models in the new paper. Paty and I were able to run... four of them. One of the models kept refusing to render, for reasons that were were never able to determine. It was maddening. Paty reached out to her colleague overseas, Jesús Muñoz, who agreed to help us. He helped not only to fix the problem, but also helped us do more types of analyses than we initially set out to do.
That Jesús was not at the same campus as us overseas made for some interesting collaborative issues, primarily getting files from point A to point B. Some of the files generated in modeling are huge, and even my trusty Dropbox folder was spitting the dummy. We went though many rounds of trying to figure out how to get the files from on computer to another. But that was eventually solved.
Something of an offhand comment by another colleague, Kristi Lowe, led to the choice of journal. She mentioned that she had just published a paper in Aquatic Biosystems. To be honest, I hadn’t heard of the journal before, but she had been very happy with the editorial process. She’s also told me that the journal had changed from Saline Systems and broadened its scope to include freshwater systems.
And they were having a sale.
Aquatic Biosystems, like many other open access journals, has a publication fee. But they were waiving the fee until the start of June as part of a promotion.
My current projects are being funded by things like my #SciFund donors (♥ you guys), and publication fees are often almost as much as entire projects cost. While I have no problems asking for a waiver, it was a good deal. I was a sucker for a bargain and decided to go for it.
I’m very happy about much of this paper: new co-author, new journal, open access, relevant to policy.
But in my perfect world, this paper wouldn’t exist. I admire papers that are comprehensive. I would have much preferred had the 2011 and 2012 papers all in one bigger, more substantive paper. But I was overtaken by events. This has happened to me a couple of times now, which is disconcerting.
But better to be overtaken by events than be stagnant.
Faulkes Z, Feria TP, Muñoz J. 2012. Do Marmorkrebs, Procambarus fallax f. virginalis, threaten freshwater Japanese ecosystems? Aquatic Biosystems8: 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 Invasions6(1): 55-67. http://dx.doi.org/10.3391/ai.2011.6.1.07
Internal versus external. It’s a constant tension between these explanations. In psychology, there’s the eternal argument about nature versus nurture. In behaviour, there was a lot of debate about whether chain reflexes or central pattern generators were the main drivers of debate. And this same argument carries on in evolution. Are certain lineages successful in creating lots of species because:
There was something about the environment they were in? For instance, an ancestral species happens upon new habitat with unfilled niches. (Speciation driven by external causes.)
They have some special feature? Ancestral species has some key innovation innovation, which is so adaptable that it allow it to diversify faster. (Speciation driven by internal causes.)
A paper by Wagner and colleagues tries to weight these two possibilities against each other using African cichlids. Several rift lakes in Africa are famous for having a lot of cichlid species in them, like Lake Victoria and Lake Tanganyika. What is less well known is that there are lots of examples of African rift lakes (created recently, so lots of unfilled niches) that were invaded by cichlids (which have some interesting features in the ways their jaws work, so lots of evolvability)... but that were not followed by a burst of evolutionary innovation for which cichlids have been so well studied (Seehausen, 2006).
This means there are a lot of natural experiments that allow you to figure out why there are somethings veritable explosions of diversity, and sometimes... matches fizzling out.
They found three factors that were most correlated with adaptive radiations: two external, and one internal.
First, the depth of the lake. This makes sense to me: the deeper the lake, the more potential niches there are for fish to inhabit. Cichlids are often very visual animals, and the changes in light quality as you descend could be an important factor in creating new niches. It’s not just size of the lake, as surface are doesn’t come out as a strong predictor. (I wish they estimated volume, though.)
Second, solar radiation. Now, I would have thought that most of these being more or less in equatorial regions that there wouldn’t be much difference in the amount of sunlight from lake to lake, but this is why you do the experiment and not count on intuition. (Additional: I was thinking of day length, but it occurred to me that cloud cover and climate would affect this, too.) They authors suggest that the greater “energy” in the system facilitates speciation.
Third, the difference in appearance of the males and female of each species is a predictor of speciation (sexual dichromatism). Why should this matter? The authors matter that it probably doesn’t, but that the difference in appearance between the sexes indicates that there is a lot of choosiness who gets some sweet lovin’ sexy time in the rift lakes of Africa. In other words, big differences in appearance means more sexual selection is going on in the population.
This may also be correlated with lake depth, since earlier studies showed that visual signals were critical to sexual selection in many of these species. In fact, there are cases when waters started to get cloudier, different cichlid species started to hybridize again.
This and other research is suggesting more and more that some evolutionary events are predictable, at least in broad strokes.
Reference
Seehausen O. 2006. African cichlid fish: a model system in adaptive radiation research. Proceedings of the Royal Society B: Biological Sciences 273: 1987-1998. DOI: 10.1098/rspb.2006.3539
Wagner CE, Harmon LJ, Seehausen O. 2012. Ecological opportunity and sexual selection together predict adaptive radiation. Nature: in press. DOI: 10.1038/nature11144
Photo by RevisionTwo on Flickr; used under a Creative Commons license.
Who could be against critical thinking? It has been the greatest tool for progress, both intellectual and economic, the world has ever known. It’s like being against motherhood. Who could be against that?
The Republican Party of Texas.
Seriously, really, it’s part of their party platform. Look on page 12.
Knowledge-Based Education – We oppose the teaching of Higher Order Thinking Skills (HOTS) (values clarification), critical thinking skills and similar programs that are simply a relabeling of Outcome-Based Education (OBE) (mastery learning) which focus on behavior modification and have the purpose of challenging the student’s fixed beliefs and undermining parental authority.
What makes this all the more jaw-dropping is this plank in their platform, just two points down:
Funding of Education – We urge the Legislature to direct expenditures to academics as the first priority.
“We want education! We just want it to be very bad education that can ensure our children are servile drones.”
My jaw is on the floor.
Additional, 29 June 2012: The Texas Freedom Network is reporting that that the Texas Republican Party is saying the plank was an “oversight.” SuuuUUUuuuuure.
They’re still worried, though, about education that “serves the purpose of challenging students beliefs and undermine parental authority.” I think any decent education challenges beliefs and undermines authority. It is kind of the entire point of education to make people into autonomous individuals who are able to navigate the world around them independently.
A Taiwanese hermit crab, Calcinus laevimanus, photographed bereft of shell. The small size doesn’t do it justice; click to enlarge.
Photo by Tin-Yam Chan, from here; used under a Creative Commons license.
Be sure to check the freakin’ amazingphoto gallery on this site. It will blow you away with wonderful diversity. It's a bit clunky to navigate, but worth it.
When I am giving a talk, I do not read from a script.
But I often write a script or notes when I am preparing for a talk. I learn a lot by looking at the page. Often, what happens is:
Picture of study species: Short paragraph, couple of lines in length.
Introduction of concept slide: Short paragraph.
Statement of hypothesis: Short paragraph.
First graph of results: Short paragraph.
Second graph of results: Three long paragraphs of notes.
When I look at a page and see the notes for one slide that are way longer than slides before and after, I know I haven’t clearly articulated the point I want to make. It’s a reliable marker that I have more thinking to do.
Sometimes, another benefit is that you can uncover just the right turn of phrase. The shorter the talk, the more important those well chosen sentences are. They will save you from chewing up valuable minutes of time explaining something.
There is a big difference between looking at your slides and thinking, “I know what I’ll say here,” and doing it. This, of course, is the same reason you need to rehearse your talk out loud. Sometimes, though, writing it out is useful when might not want to say all that stuff out loud. You’re not ready yet, don’t have a quiet space, or whatever reason.
Writing a script for a talk forces you to be explicit, which reveals your weaknesses. That makes it useful, even if you never read from it on the day.
I’ve had a free PDF called Presentation Tips available for a while now (available on my homepage). I recently got my hands on a proper ebook reader (a first generation Nook), and decided to see how it looked there.
I was underwhelmed. I hadn’t realized how ebook readers handled PDF files. It was okay. It was certainly readable, but I thought, “This could be better.”
As I tried to figure out ebook formats, one thing lead to another and, well... Today, I’m pleased to announce that you can buy Presentation Tips on Amazon.
US store(Um. Embarrassingly, showing as “not available” yet. This apparently happens occasionally and should sort itself out.)23 June: Sorted and ready for purchase!
My main goal was to do this for people who wanted a proper ebook version, but I decided to go the extra step to publish this on Amazon for a couple of reasons.
One was curiosity about how much of an audience I could reach by being on Amazon. I know full well that not everyone reads this blog. The positive feedback I received, largely from people on Twitter (thanks, guys!) convinced me that there was enough useful information here that maybe it was worth trying to present it on a bigger stage.
Second, I want to see how university administration will react when I put this in my merit folder. I think I can make a good case that this book is a peer-reviewed (they’re tweets, but from people with solid academic credentials) and published by an international publisher (Amazon will make this available around the world). According to our guidelines for achievement, a peer-reviewed book from an international publisher is worth a lot of merit points. But our guidelines are at least ten years old, and people have been reluctant to tinker with them.
I make no bones that publishing Presentation Tips as I have is clearly a different process than what was possible (and intended) when the guidelines were written. I’d like to press a little to see to how people will interpret our existing guidelines.
Third, this is sort of a dry run for some other, bigger projects I have percolating in the back of my head.
On the other hand, there’s this wonderful post about a self-publishing success story from Jessica Park. I was already sure I was going to put Presentation Tips on Amazon, but that article pushed me a little more. Park talks about the frustration of waiting to be chosen. I mentioned this the start of the last round of #SciFund.
It struck me that so many scientists are still in the place artists were. We’re waiting to be chosen. Waiting to be given permission. Working and working and working in the hope of being given a shot at the big time by someone else with more money, power, and influence.
Self-publishing Presentation Tips is another little “What will happen if...?” to see if I can carve out an independent path. Indeed, a little revenue coming in from this might allow me to self-fund some of my research projects, complementing endeavors like my #SciFund crowdfunding.
The price is modest: $2.99. Why didn’t I make the ebook version free, like I had with the PDF? Well, I did do quite a bit of work to make this a proper ebook, for one. It’s not just a straight dump of blog posts or the already available PDF. The ideas within are, and will always be, free. You can read the Zen of Presentations blog posts here, and I’ll keep the PDF available too. I’m only asking you to pay if you want the convenience of the ebook version, or if you want to support your local Crab Clan Scholar.
If you read this in any version, please rate it on Amazon!
Lovecraft might have liked this new paper by Frank and colleagues, since he though squid-like beings could dream...
In his house at R’lyeh, dead Cthulu waits dreaming.
Sleep is a surprisingly thorny behaviour to explain. Why should an animal stop attending the world around them (or, to put it in human terms, losing consciousness), leaving itself vulnerable to how knows how many shocks and threats?
Research on human sleep has defined and driven sleep research. The question of invertebrate sleep, for example, was very slow to develop because of the problems in comparing invertebrate neurophysiology to vertebrate neurophysiology. Research on human sleep had been revolutionized by the Hans Berger’s introduction of electroencephalography (EEG), which allowed us to see the differences in brainwaves during sleep. EEGs defined sleep research so much that one researcher I know was told that she could not say an invertebrate was sleeping because there were no records of brain waves, regardless of what the behaviour was.
Cephalopods are potentially very interesting subjects for sleep research because of their brainwaves. When you try to record brainwaves from most invertebrates, you get very spiky recordings rather than waves. Cephalopods, and particularly octopuses, have brain waves that are more vertebrate like: wavy, not spiky (Ted Bullock wrote about this quote a bit). So for those who define sleep by changes in brain wave activity, cephalopods may offer more points of comparison.
This new paper by Frank and company doesn’t have brainwaves, but could be an important first step in developing methods to study sleep in cephs. They do two things here.
First, they document that cuttlefish go through periods of behavioural sleep: prolonged inactivity. They call this an experiment, but there isn’t any manipulation, so it’s really just a study. They do document some intermittent behaviours that they argue are analogous to rapid eye movement (REM) sleep in mammals, though I don’t buy that at all.
The second experiment is much more interesting. I’m sure everyone has had the experience when you don’t get enough sleep. When you’ve been deprived of sleep, the next time you do sleep, you sleep more than normal. That “rebound” is evidence that the inactive state is sleep and not just inactivity.
So Frank and company sleep deprived their cuttlefish. Now, sleep depriving an animal is a very tricky business. How do you stop a cuttlefish from sleeping?
This was one of those rare times I was glad I read the methods section.
A vertically-facing LCD computer monitor was positioned beneath the bottom of the tank. Hans Zimmer’s “King Arthur” film score (2004) was played (Microsoft’s Window Media Player) and the visualizer option was used to project random shapes on the screen. Angled mirrors placed around the sides of the tank reflected the screen image all around the cuttlefish to ensure constant, gently moving visual stimulation.
That’s... oddly specific.
Regardless of their choice of film scores, Frank and company did indeed find that after being prevented from “sleep,” their cuttlefish did indeed sleep more when next given the chance.
This is a very cool and promising start on sleep research in cephs. But I’ll tell the authors this for free: if you want to push this further and catch the attention of mainstream sleep researchers, you’re going to have to record brain activity. It will be maddeningly hard, but if you can get those data, that’s when things will start to get fun.
Additional, 23 June: I have an answer to the question I posed in the title!
Reference
Frank MG, Waldrop RH, Dumoulin M, Aton S, Boal JG. 2012. A preliminary analysis of sleep-like states in the cuttlefish Sepia officinalis. PLoS ONE 7(6): e38125. DOI: 10.1371/journal.pone.0038125
Cuttlefish photo by Eric Burgers on Flickr; used under a Creative Commons license.
Can natural selection act on groups of individuals?
This is a decades-old argument in evolutionary theory that many thought was settle late in the twentieth century, but it has recently reared its head again.
One of the lead proponents of resurrecting group selection has been E. O. Wilson. You can read reports of Wilson’s recent presentations here and here. Steven Pinker recently jumped into the fray.
Almost everything that I read on both sides of this issue is highly conceptual stuff. Models are formulated. Reasons are advanced. It’s all very abstract and with a lot of jazz hands. It’s been frustrating for me, and keep in mind, I like this stuff. I’m co-teaching a graduate class in evolution right now. I can’t imagine what a non-specialist makes of this stuff.
Largely absent in these discussions are terms like “hypothesis,” “prediction,” and “test.”
What I would love to see would be for those in this argument to say, “Here is an organism with that routinely lives in groups and benefits from being in a group. If group selection is occurring, we would expect to see this much more reproductive success than you could account for by individual success alone.”
If not reproductive success, gene frequencies, or some other measures.
And I would love to see these experiments made for animals other than humans. There are too many pitfalls that can trap even the wariest researcher when thinking about humans. Meerkats might be a good case study, if this interview with Tim Clutton-Brock is anything to go by. He rejects kin selection as the main explanation for cooperation in meerkats.
I started off thinking that the whole thing ran through kinship. Kinship is obviously there but these group-related benefits are obviously fantastically important, and my suspicion is that in most of the highly co-operative mammals, things like naked mole rats and African wild dogs, the same pattern holds. They're related to each other, but there are lots of other social mammals that are related to each other which aren’t advanced co-operators. And the unusual thing of the advanced co-operators is that they live in habitats and they live in ways where they’re really dependant on other members of the groups.
Note, though, that “benefiting from being in a group” – which Clutton-Brock is describing – is not the same as “group selection.”
Those who are advocating that group selection is a major evolutionary force need to articulate a research program.
The value of having a research program is often underestimated. It’s not enough to be right in principle; you have to suggest experiments that you can do to test them. A lot of experiments.
For example, there are a lot of different ideas out there for how to define species. But the biological species concept (species are non-interbreeding) suggested a research program while other species concepts did not (Coyne and Orr’s Speciation). The discovery of a major impact at the K-T boundary ( Alvarez et al. 1980)suggested a research program. Eldredge and Gould’s punctuated equilibrium (1972) suggested a research program, and lots of productive science arose from that. Gould and Lewontin’s Bauplan (1979) didn’t readily suggest experiments, and languished.
Wilson developed a research program when he published Sociobiology (1975). That book (perhaps along with The Selfish Gene; Dawkins 1976) galvanized animal behaviour. Ethologists probably spent a good 15 years or so exploring and testing ideas arising from those books.
I have only vague ideas about what a group selection research program would look like. But then, it’s not my job to spell out the research to do: that burden lies with those who are advocating group selection is important in evolution.
Additional, 24 June 2012: The Guardianhas noticed. They frame this as a “Let’s watch the famous guys fight,” though, which is disappointing.
Alvarez LW, Alvarez W, Asaro F, Michel HV. 1980. Extraterrestrial cause for the cretaceous-tertiary extinction. Science 208: 1095-1108. doi: 10.1126/science.208.4448.1095
Coyne JA, Orr HA. 2004. Speciation. Sunderland, MA, Sinauer Associates.
Dawkins R. 1976. The Selfish Gene. Oxford, Oxford University Press.
Eldredge N, Gould SJ. 1972. Punctuated equilibria: An alternative to phyletic gradualism. Models in Paleobiology. TJM Schopf (ed.), pp. 82-115. San Francisco, Freeman, Cooper and Company.
Gould SJ, Lewontin RC. 1979. The spandrels of San Marco and the Panglossian paradigm: A critique of the adaptationist programme. Proceedings of the Royal Society of London. Series B. Biological sciences205(1161): 581-598. DOI: 10.1098/rspb.1979.0086
Wilson EO. 1975. Sociobiology: The New Synthesis. New York, John Wiley.
Photo by Digimist on Flickr; used under a Creative Commons license.
This week’s crustie is a European river crab (besting a vertebrate - ha!) named Potamon fluviatile. Rob Dunn has an excellent post on the Scientific American Guest Blog about a population living under the streets of Rome that might just be a new species.
Filed under the category of “interesting things neurons do...”
A forthcoming paper by Favero and colleagues showed how motor neurons compete with each other for synaptic “real estate.” The fastest, most effective way for a “winner” to be decided was not to have the two neurons firing “head to head” at the same time, as the figure below shows (a composite of parts of the their Figures 1 and 2):
First, let me explain what “polyneuronal innervation” on the left Y axis means. Favero and company were working with rats. Normally, muscle cells in mammals (including rats) have just one motor neuron connected to them and controlling contraction in that muscle cell. But you can create a situation where more than one neuron innervates a muscle cell temporarily. That’s polyneuronal innervation, given in the left label.
The muscle here is the rat soleus muscle, which is innervated by two nerves. The team crushed the two nerves leading to the muscle, and the nerves grow back to rejoin the muscle. When they do so, the neurons don’t neatly divide up the muscle cells immediately. Many of the muscle cells get neurons from both nerves innervating them. You can see this polyneuronal innervation in this picture (their Figure 5):
The key things are the three “blobs” that show a mix of red and green. Those are the synapses between the muscle and the neurons. Neurons from one nerve are stained red, and those from the other are stained green.
This is not normal for adult mammals, and so you want to get rid of the polyneuronal innervation.
The researchers were able to control when the nerves innervating generated action potentials through a series of complicated interventions.
When the nerves were fired 20 ms apart or more (black bar at right in the top picture), you got much less polyneuronal innervation than when the nerves were fired at the same time (red bar at left).
Favero and colleagues do a series of experiments to show that the key factor here is the timing of the two signals, not just the muscle activation. They also showed that the relative number of spikes is also playing a role in determining how quickly you can get rid of those polyneuronal connections.
How general this phenomenon might be depend on how important competition between neurons is for determining synaptic connections. This polyneuronal innervation is not normal for adults, but the authors mention you do see it during development, so this is not a completely artificial scenario. Some authors, notably Gerald Edelman, have proposed that neuronal competition is a key element in shaping vertebrate brain circuits. This finding may have broad implications, but we’ll need some more good systems showing neural competition to test it.
Reference
Favero M, Busetto G, Cangiano A. 2012. Spike timing plays a key role in synapse elimination at the neuromuscular junction. Proceedings of the National Academy of Sciences: in press. DOI: 10.1073/pnas.1201147109
This post by Dererk Lowe bugs me. And I might have let it slide, but then it got picked up by Discover Magazine, and I was annoyed all over again.
(M)ediocre scientists are, in fact, in long supply. Access to them is not a rate-limiting step. ... Who, exactly, would be clamoring to hire a fresh horde of I-guess-they'll-do science graduates? Is that what we really need to put things over the top, technologically - more foot soldiers?
... My emphasis would be on "How do we get the smartest and most motivated people to go into science again?". ... When someone seems to be born for a particular field, like R. B. Woodward for organic chemistry, I want them to have every chance to find their calling.
This implies that:
Great scientists are easily identified.
Great scientists are inherently attracted to science.
Science progresses by breakthroughs made by great scientists.
Let me deal with these in turn.
“Great scientists are easily identified.” You know how we identify great scientists? Retroactively. Scientists are not deemed great because of their potential; they’re deemed great because of their work, often years after it was done. I’ll ask senior people who have tracked careers of their students: How many people have you seen who you thought were promising, and then watched them struggle at various times in their career? Some people fizzle out, and others are late bloomers. Charles Darwin would not be acclaimed as a great scientist if he’d had the misfortune to succumb to his poor health at age of 48, before publishing On the Origin of Species.
“Great scientists are inherently attracted to science.” I hate this notion that science is a “calling,” that that some people are just destined to do science. This implies that if you don’t feel the love for science at the very early age, it’s not for you. Sorry, you weren’t “called.” How many people learned that they enjoyed science only when they got into a lab with a great teacher?
This myth of destiny and inevitable triumph of genius is, to me, completely the opposite of what science is. The scientific method leveled the playing field for discovering truth. Anyone could follow the methods and get to the bottom of things, so truth was no longer subject to tricky things like personal revelation.
“Science progresses by breakthroughs made by great scientists.” Or, to use another of Derek’s analogies: what is the rate-limiting step in science? Derek says we don’t need more “foot soldiers.” In a comment on his original post, I noted that soldiers win wars. If they have bullets and body armor. They need resources. I contend that lack of resources are the rate-limiting step now in scientific advance (and I include employment opportunities as resources). Science isn’t limited because we have too many mediocre scientists who don’t have bright ideas; we have too many scientists who aren’t given the resources to do the science they want.
The “great scientists” trope also ignores the loose relationship between quality of science and quality of scientists. It’s almost a standing joke about how Nobel prize winners go off the rails and start advocating crazy woo after winning the award. Many bright scientists toil away on ideas that happen to wrong. The obsession with being first to publish means that if you develop a better mousetrap, you are more likely to be recognized as a “great scientist” even if other labs working on the science were just slightly behind in making the same discovery.
I’ve written before many times about the incremental nature of science. And there’s also this idea that you can get solutions to problems by going at them head-on. And it may not be that way. Neil deGrasse Tyson often talks about how so many breakthroughs came from unexpected sources. Advances, he argues, come from curiosity driven research. I don’t buy that entirely; I think a mix of approaches is better.
Astronauts and the bedridden have one thing in common: they have to be very concerned with their muscles. When muscles don’t work, they shrink. So after a few moths in freefall, astronauts come back to Earth weak. Muscles truly are, “Use it or lose it.”
How do bears spend months not moving and then wake up far from weak?
This new paper by Lin and colleagues is a nice, simple strong inference test of two competing hypotheses of how bars keep their muscle tone over winter.
With neurons. That is, bears use their nervous system to periodically activate their muscles and shivering.
Without neurons. Intrinsic resistance to atrophy within the bear’s muscles, by activating some signalling pathway.
Conceptually, the experimental test is easy: remove neural signals from bear’s muscles. The hard part is carrying it out. Working with bears is not like working with lab mice. The brown bears (Ursus arctos) here were all bears that had been captured. They knocked the bears out, and measured the size of ankle muscles using ultrasound before cutting the nerve in the left leg. They did sham surgery on the right, so each bear acted as its own control.
They did five of these surgeries at the start of summer, and five at the start of winter, so Lin and colleagues were able to compare seasonal effects.
Muscles shrank after surgery in both seasons, but much less so in winter. The second hypothesis wins out: the nervous system isn’t responsible for the bears maintaining muscle tone. The bears have some other mechanism going on here. Time for the neurobiologists to hand over to the muscle physiologists for the bulk of the research on atrophy resistance.
The neurobiologists might not be entirely out of the picture, however. I would have thought that the muscles’ resistance to atrophy might be constant year round. That muscles atrophy in summer but not winter sows there are some kinds of signals from some source that are regulating seasonal cues. Day / night length is an obvious candidate, or environmental temperatures. The nervous system might be involved in the early regulation of the muscle condition.
Reference
Lin D, Hershey J, Mattoon J, Robbins C. 2012. Skeletal muscles of hibernating brown bears are unusually resistant to effects of denervation. The Journal of Experimental Biology215(12): 2081-2087. DOI: 10.1242/jeb.066134
Photo by Li'l Wolf on Flickr; used under a Creative Commons license.
The debut of Prometheus spawned a surprisingly large amount of attention in my scientific social network this weekend. This proves that scientists are not attracted by circus afros, I guess.
I’ve reviewed the film on its artistic merits on Sunday Matinee, my movie review blog.But I thought it would be fun to talk about some of the biology in the film. I’ll leave the astronomy (which I have my suspicions about) to others.
Spoilers ahead, so discussion continues below the fold:
