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Microbiomes mediating microevolution

Bacteria. Is there anything they can’t do?

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

Photo from Cho et al. (2011), used under a Creative Commons license

Big in Japan

This is not a paper I wanted to write.

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.

Related posts

Potential invasions anew new horisons
How my ethics of brain scanning paper was overtaken by events

References

Faulkes Z, Feria TP, Muñoz J. 2012. Do Marmorkrebs, Procambarus fallax f. virginalis, threaten freshwater Japanese ecosystems? Aquatic Biosystems 8: 13. http://dx.doi.org/10.1186/2046-9063-8-13

Feria TP, Faulkes Z. 2011. Forecasting the distribution of Marmorkrebs, a parthenogenetic crayfish with high invasive potential, in Madagascar, Europe, and North America. Aquatic Invasions 6(1): 55-67. http://dx.doi.org/10.3391/ai.2011.6.1.07

Adaptive radiation: driven by circumstances or inner potential?

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.

Related posts

How’d you get that fat lip?
Laying down boundaries for brain evolution in cichlids

Who could be against critical thinking?

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.

Spotted at I’m Not Really Here.

Tuesday Crustie: What’s under that shell?

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’ amazing photo gallery on this site. It will blow you away with wonderful diversity. It's a bit clunky to navigate, but worth it.

The Zen of Presentations, Part 55: Script doctoring

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:

1. Picture of study species: Short paragraph, couple of lines in length.
2. Introduction of concept slide: Short paragraph.
3. Statement of hypothesis: Short paragraph.
4. First graph of results: Short paragraph.
5. 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.

“Sure, he can walk on water, but his GRE scores were rotten...”

“Man, I thought Jesus would never finish his Ph.D.”

“You know his committee just passed him because he kept the departmental seminars flush with bread and wine.”

“Maybe, but he’s had good success as a PI. He’s got a big lab now, with twelve grad students.”

“Yeah, but I hear there’s trouble brewing with that one student, Judas, who’s going to lodge a complaint against him with the Dean.”

Spotted on Academic Tree – Philosophy branch, specifically..

Presentation Tips for Kindle

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.

• UK store
• French store
• German store
• Italian store
• Spanish store
• 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.

It’s a weird time to try this. On the one hand, the low bar for self-publishing keeps dropping lower. I hope Presentation Tips has more value than bots scraping YouTube comments and self-publishing them as books.

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!

Do cephalopods dream of aquatic sheep?

A ScienceSeeker Editor’s pick!

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.

Group (selection) therapy

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 Guardian has noticed. They frame this as a “Let’s watch the famous guys fight,” though, which is disappointing.

Additional, 25 June 2012: Jerry Coyne is disappointed by The Guardian piece.

References

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 sciences 205(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.

Tuesday Crustie: Under the streets of Rome

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.

Photo from here. Hat tip to DNLee5.

Compete off-beat to delete!

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

Picture from here.

That’s my dad!

These were taken by my mom on Father’s Day last year.

Happy Father’s Day!

Comments for first half of June, 2012

Jeanne Garbarino looks at reaching our from the universities. There are similar issues that I raised in my interview on The Critical Wit on science crowdfunding.

Tom McRae has advice to authors of research article.

Derek Lowe, at In the Pipeline blog, looks at the over-production / under-production of scientists.

Miriem Goldstein offers a flowchart for online science outreach.

The subject of outreach also comes up at Matter Tomorrow.

Dr. 24Hours has ever vexing grant questions.

Ars Technica examines the launch of PeerJ, a new open access journal with an unusual pricing scheme.

In Baby Attach Mode asks how you come up with grant ideas.

The genius myth

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:

1. Great scientists are easily identified.
2. Great scientists are inherently attracted to science.
3. 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.

Related posts

Tales to astonish
I’m a pebble in the avalanche
What the Coburn report has in common with arsenic life

External links

Imposters, underdogs, and the status of science

Photo by quinn.anya on Flickr; used under a Creative Commons license.

Keeping strong during a long winter nap

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.

1. With neurons. That is, bears use their nervous system to periodically activate their muscles and shivering.
2. 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 Biology 215(12): 2081-2087. DOI: 10.1242/jeb.066134

Photo by Li'l Wolf on Flickr; used under a Creative Commons license.

Tuesday Crustie: Look up, look waaaay up...

Described as an “Atlantic ghost crab” by the photographer, which is probably Ocypode quadrata.

Photo by Mark Sinderson on Flickr; used under a Creative Commons license.

The biology of Prometheus

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:

A moment of Bradbury

Of course I read Ray Bradbury.

I read some because I had to (they were assigned in school), but somehow that that didn’t reduce my enjoyment of them.

I distinctly remember a drawing I made in school of a long-necked plesiosaur in the ocean next to a lighthouse. I remember the plesiosaur on the left, and the lighthouse on the right, and I think the plesiosaur was grey. I pictured most ancient reptiles and dinosaurs as having leathery grey hides then. I liked plesiosaurs, because they were so often invoked as explanations for sea and lake monsters, like Nessie. It was the scene from Bradbury’s story “The Fog Horn”.  

The Beast From 20,000 Fathoms depicted the same scene. Ray Harryhausen’s Rhedosaurus was rather different than my long-necked, flippered sea reptile, though. Being able to walk around on land certainly made for a much more entertaining movie.

The Beast from 20,000 Fathoms was one of the direct inspirations for the first Godzilla movie. This makes Ray Bradbury Godzilla’s godfather. And those movies inspired the main video for my recent #SciFund, “Beach of the Goliath Crabs.”

Ray Bradbury, 1920-2012.

The root of problems

Why aren’t scientists rewarded for outreach? As Scicurious and Kate Clancey’s posts yesterday.point out, academics are pushed hard to do research, and are frantically busy people as a result. But why are they pushed so hard to do research in particular?

To answer that, we have to examine some deeply embedded structures.

Probably many people who have a passing familiarity with science or universities know that in the United States, much research is supported by grants from the federal government. What is less well known is this aspect of grants that are variously called “overhead” or “indirect costs (IDC).”

If I write a grant, I estimate how much the research project will cost me and write up a budget. I put in salary for students, costs of supplies, travel, and maybe some money to pay publication charges when the work is done.

I get a total. A nice, even, $50,000, say. Then, the university takes that total and adds overhead costs to it. Suddenly, the cost goes from $50,000 to $75,000 or even more. Typically, the bigger and swankier the university, the bigger the proportion of overhead.

Overhead is supposed to ensure that the institution supplies the researcher basic infrastructure. The phrase I’ve sometimes heard is that overhead helps to ensure the university “keeps the lights on.”

I do not know how or when the practice of including overhead in grants began. But I think it’s had some bad effects, which were probably not intended.

Overhead changes the dynamic in play for research tremendously. Because it gives institutions a particular kind of financial stake in research outcomes, and that twists the focus away from productivity towards profitability.

Let’s say you have two researchers. Both are publishing papers at the same rate. One person does mostly expensive bench research, the other is more a theoretician. Overhead makes it almost inevitable that the first person will be more valued because they bring in more dollars to the university, regardless of the relative amount or quality of the scholarship.

Overhead may be the root cause of the relentless push from university administration for their faculty, particularly new faculty in the tenure process, to do almost nothing but research.

Overhead distorts the way administrators measure research success: not by papers, or citations, or any other sort of measure, but by dollars. I’ve read more than once that some universities are outsourcing their tenure decisions to grant agencies. Didn’t get a grant? You’re fired. (Never mind that the proportion of grants getting funded at most agencies is at all-time low.) This can trump being a productive researcher by any other measure, like publishing papers. That pushes teaching off the radar, and outreach even further away.

Overhead creates perverse disincentives for particular kinds of funding. When we did a Google Plus hangout on crowdfunding last week, we talked for just a few second about how universities were not likely to support crowdfunding because they don’t get a big cut of the money raised. So you have this weird situation that institutions can be actively discouraging their faculty from pursuing money to do research – in a time when everyone is gasping for ways to support research – because the university wants money.

Now, I am sympathetic to the institutions and administrators. Finances are bad for a lot of universities. Pushing faculty as hard as you possibly can to get grants that bring in money is entirely rational, particularly given declining support, particularly public universities.

Overhead solves some problems, but has created others. And it’s so deeply embedded into the current granting structure in the United States that it’s hard to envision how it could be extricated or reformed. But it does not have to be that way. In Canada, it used to be that every nickel of a research grant went to the researcher (not sure if that’s still true). This was possible because there was greater provincial support to the universities.

Tuesday Crustie: Yuruginai

Art by Steve Argyle. From the L5R art Tumblr, which writes about this art:

The biggest of the Celestial Swords, embedded with jade, reforged and the Celestial Sword that’s seen the most action. Even the saya is sturdy enough to be used as a weapon. It has one of the longest handles indicating military use over style as well.

This one may end up in the blogs’s masthead one day.

Nailbiter

Round 1 of #SciFund was a rollercoaster.

Round 2 of #SciFund was a nailbiter.

About a week ago, I wrote on the #SciFund blog:

I can’t wait to see what the final week wolds. Can we hit a six digit total? At the rate we’re going, that’s not impossible.

Little did I know.

Last Friday, we passed the round 1 record of $76,230. Then, we passed $80,000, which made a combined total of $150,000 for both rounds of #SciFund and 30 funded projects. That got some attention, I can tell you. Then we had five projects hit their targets in one day.

And with just one day to go, we passed $90,000.

The possibility of $100,000 was tantalizing, but I knew raising $10,000 in a day was going to be a big ask.

During the day, while I kept obsessively checking the total, tweeting about projects, and posting on Google Plus, I kept thinking about an episode of Top Gear (Series 4, Episode 4), in which host Jeremy Clarkson has to drive from London to Edinburgh on one tank of fuel. He’s getting closer and closer to the finish, but knows he’s running out of fuel. And when he get so close to the end but not quite there, he says, “If I don’t make this, I’ll sack myself.” (Sacked as in fired.)

That’s what I felt like. That at any second, this car is going to run out of gas and we’ll be stuck on the road, embarrassed by the failure.

And yes, it would have felt like a failure. My nightmare was that we’d get to $99,999 and time would run out. (I almost need not have worried quite so much, as there are still six projects with hours to go.) The difference between $99,999 and $100,000 is not $1, psychologically speaking. Salesman have known this forever, which is why you see so many prices like $1.99 or $499.

Intellectually, $99,000 and change would still be a great success. But emotionally, it would have been one of those, “We were this close...” moments that haunt you.

Later that night, the next image that came to mind, just before and after I was doing a Google Plus hangout with SciLingual, was that this felt like a bomb ticking down in an action movie. Except that in an action movie, you’re generally sure someone is going to step in before it’s too late.

I had no such confidence here.

Other things that were rattling around in my head were the success of Amanda Palmer, fellow crowdfunding traveler in the month of May (who raised ten times what we did), and the safe return of the SpaceX Dragon to earth. It seemed to me that these, and #SciFund, were all culminations of... triumphs of small over big.

But the amount we needed kept getting smaller. Less than $5,000. Less than $2,000. (A few hours left. The tension is killing me.) Only hundreds. (Only minutes left for most projects. Jarrett is updating the totals every few minutes.) $33! (Projects are just about to start closing!)

Last night, at 11:01 pm my time, I saw this:

I was pleased.

I was also pretty emotionally spent. It was quite late and I would have happily gone to bed... but #SciFund kept calling. There was data I needed to gather about the completed projects pretty much right then, so I couldn’t go to sleep. And there was some loose ends. Like having to blog all this while it’s still fresh.

Tomorrow, I want a press release. We showed that #SciFund was no one trick pony. And with so many projects funded (30 some odd - I’ve lost count) and the important $100,000 total, we can bring some attention not just to science crowdfunding, but science funding and science engagement generally.

But I think it’s finally time for bed.




Update: Favourite analysis of #SciFund this morning, courtesy of Eddie Cardoshinsky Google Plus:

It's like the new Muppet Movie, but only for science.

Comments for second half of May, 2012

Bradley Voytek tries to track down the longest axon.

Ah, there’s always fun to be had when Drugmonkey looks at journal publication. This time, it’s about costs of publishing in open access journals.

The Mermaid’s Tale looks at a commentary on innovation that I blogged about earlier.

Tom Webb, writing on the Mola Mola blog, is ambivalent to open access.

Fighty Crab and I make cameos in the Comprendia blog in looking at photos in life sciences. And I get a quick mention at The Thoughtful Animal on octopus navigation (a re-post, but maybe you’re one of today’s lucky 10,000.)

A Blog Around the Clock and Profhacker were also both nice enough to give this blog a mention.