Better off blind

Eyes are good things to have in the light. But if you lived in the dark... all the time... would those eyes become so much a nuisance that you might lose them?

Animals that live in caves are often blind. People sometimes mistake this as evidence that features can be lost just by a “Use it or lose it” rule. That would be an example of inheriting an acquired character, which doesn’t happen in evolution. Instead, the typical explanation is that because there is no advantage to maintaining eyes if you’re a cave dwelling population, any mutation that messes up making eyes is on an equal footing with the genes for making eyes.

It’s not that there’s an advantage for blindess... it’s just that there’s no disadavantage to it. And eyes are complex things to make, so lots of mutations could interfere with making eyes.

A recent paper by Klaus and colleagues suggests that sometimes, blindness in a cave-dweller is an advantage, not just neutral. They examined a group of crabs (genus Sundathelphusa; pictured, showing most cave adapted at bottom) in the Philippines. These are freshwater crabs, and some live in lakes and rivers and such above ground, and some live in caves. In fact, these crabs invaded caves over half a dozen times in the genus. The repeated examples make for nice natural experiments.

Using a combination of genetics plus the shape of the animal, they found that the eyes of the cave crabs had evolved just as fast as other features. Klaus and company argue that if the loss of eyes was genuinely neutral, you would expect it to be happening more slowly than other features, which are presumably under selection. Instead, the eyes were evolving just as quickly as the other featured, which suggests there is some sort of advantage to being blind.

What the advantage might be... the authors don’t say, surprising. In the introduction, Klaus and colleagues mention the idea that losing eyes “frees up” compuational power for other sensory organs. But they don’t follow that up in the discussion. They don’t even speculate a tiny little bit in the discussion. Other papers have also suggested some sort of advantage to blindness, but as far as I know, nobody has yet come up with a testable hypothesis. That it seems to be the case with both vertebrates and invertebrates suggests that whatever that selective factor is, it is very general.

Additional, 17 April 2013: Another take on this paper is at Mostly Open Oceans.

Reference

Klaus S, Mendoza JCE, Liew JH, Plath M, Meier R, Yeo DCJ. 2013. Rapid evolution of troglomorphic characters suggests selection rather than neutral mutation as a driver of eye reduction in cave crabs, Biology Letters 9(2) 20121098. DOI: 10.1098/rsbl.2012.1098

Related posts

Turning light and going blind: A tale of caves and genes
Once more into the cave

Blockbusters and telenovelas: models for science communication

This week has seen a couple of headlines where not surprising things were gussied up to look like very big deals. I’ve already written about the “Darwin had emotions!” headline, and yesterday, a piece about saying “Evolution without adaptation!” was making the rounds. When I read the headlines, I made a face, as it was dangerously close to the sort of “Darwin was wrong!” headlines we’ve seen before. Sure enough, the article is about genetic drift, which is well known to working scientists. The original scientific paper about ring species is interesting,  but the Wired piece was making it seem more unusual than it was.

This is a recurring issue in science coverage. The dominant way people try to push a scientific story into the media is to sell it like this:

Science as summer blockbuster movie. This is the model that sells every story in science as a breakthrough, and that those are the only things worth our attention.

But the reality is that much of science is not about breakthroughs. It’s about slow progress.

For instance, at the recent NESCent conference (Storify here), the ENCODE project was criticized for trying to present itself an important breakthrough finding about junk DNA. The ENCODE team tried to position itself as a summer blockbuster when it wasn’t. There are lots of other examples. Another case in point: that irresponsible Time magazine cover this week, saying it was “now possible” to “cure cancer.” Wrong.

Claims of imminent breakthrough after breakthrough are going to bite us. .
There is a mode for storytelling that is more like most science.

Anyone who has every watched a soap opera or a telenovela knows that on any given day, not a lot happens. Plots advance not in single episodes, but drawn out over weeks, if not longer. The running joke is that someone stops watching a soap, comes back after months or years, and says, “I can’t believe that Robert still hasn’t confessed his love for Alice and broken it off with Britney!” There is a often a huge cast of characters, sometimes with only mildly interacting stories.

Why do people come back to soap operas, and other sorts of long form storytelling, where arcs are drawn out over months or years? The characters.

This is one reason why I think blogging and social media for scientists is so important.

I didn’t realize it at the time, but things like the old Science Blogs site (before the Pepsi implosion), and other independent science bloggers I started following around that time, became my scientific soap opera. There was a cast of interesting characters, each with their own quirks and obsessions. And you could see their progress over time. It’s been great to watch people graduate from their degrees and make it into post-docs, and move from post-docs to tenure-track positions. Some people come, some go, and others make dramatic returns to the blogosphere (though no cases of amnesia yet).

If scientists are willing to present themselves as real people, with their own interests and problems and good times and bad, we don’t need to try to convince everyone that the only reason to pay attention to us is because we’re going to save the world from an alien invasion.

Related posts

No, Charles Darwin was not a robot
Not every radical idea is right
The genius myth
Tales to astonish
Original and transformative
What the Coburn report has in common with arsenic life

External links

Something other than adaptation could be driving evolution
Oh geez, not another exoplanet story
Can science become too big to fail?
Yet-another-genome-syndrome
How pigeons cured my case of YAGS
Worst magazine cover of the year?

A short tale about a very short tail

As I’ve mentioned before, scientists are so conservative that when you see an adjective like “extraordinary” in the title, you should at least open up the paper if you can and have a peek.

I came across a paper titled, “An extraordinary tail – integrative review of the agamid genus Xenagama” in Google Reader ^*. I was a bit curious (and miffed) because I had no idea from the title what kind of organism this paper would be about. All kinds of animals have tails.

I love me spikes and spines and armor on critters, so I flipped out a bit when I learned this belonged to the Xenagama:

That is indeed an cool looking lizard (Xenagama taylori) with a cool looking tail. The genus Xenagama originally contained two species that was defined by this short, club-like, spiky tail. But there’s a problem when you use a single extraordinary feature to classify animals: you might overlook all the other features that tie it to other relatives.

A new paper Wagner and colleagues uses a lot of different tricks to tease apart the evolutionary relationships of the lizards in this genus: morphology, genetics, climate, and so on.

By looking at all the morphology, and not just the tails, they found that a long-tailed lizard previously put in another genus (Acanthocercus zonurus; below) sorts out with Xenagama and not Acanthocercus. Genetic analysis on this species also put it in with the rest of the Xenagama group, although it’s an early offshoot from the tree of these related lizards.

The authors also discovered a new species in the genus, that, like Acanthocercus zonurus, has a reasonably long tail; sort of intermediate between the short known species and the misidentified one. This new species is dubbed Xenagama wilmsi.

It turns out that the short tail of most of the lizards in this genus was something that was obscuring some of the relationships. There were similar problems with data on breeding colours. Some of the males in this group show different colours, which was used in creating their classifications, but the males don’t show those breeding colours all year round.

All of which doesn’t answer the obvious question: why do some of these lizards have these short tails? The tails do seem to have an adaptive function. The two species with long tails seem to be tree dwellers, while the two short-tailed species are rock-dwelling burrowers. Xenagama taylori will use its short spiked tail to close its burrow, which you can see in action below:


How this tail has been molded through development and genetic to get so short would be a great doctorate for someone. While native to northern Africa, some of these lizards seem to be fairly available in the pet trade. Don’t know how easily these lizards would be to breed in captivity, though.

Update, 29 March 2013: When readers think of better titles than me: Malcolm Campbell dubbed this article, “Get shorty.” Brilliant!

^* You know, that allegedly useless service that absolutely nobody needs because all of the people on Twitter and social media are so good at finding stuff that I want to read, yet who somehow let me down on discovering this.

Reference

Wagner P, Mazuch T, Bauer AM. 2013. An extraordinary tail - integrative review of the agamid genus Xenagama. Journal of Zoological Systematics and Evolutionary Research: in press. DOI: 10.1111/jzs.12016

Top photo from here; Acanthocercus zonurus from here.

No, Charles Darwin was not a robot

The BBC has this headline about some new letters by Charles Darwin that have not been published before:

Charles Darwin letters reveal his emotional side

This headline was apparently written by someone who has never read anything by Charles Darwin.

Anyone who has read Darwin’s work could criticise it many ways, but “emotionless” is not one of his faults. There’s passages like his story of holding a beetle in his mouth, showing his self-described “zeal”:

I will give a proof of my zeal: one day, on tearing off some old bark, I saw two rare beetles and seized one in each hand; then I saw a third and new kind, which I could not bear to lose, so that I popped the one which I held in my right hand into my mouth. Alas it ejected some intensely acrid fluid, which burnt my tongue so that I was forced to spit the beetle out, which was lost, as well as the third one.

Or, more seriously, look at what he wrote about his daughter Annie (small snippet):

We have lost the joy of the Household, and the solace of our old age:— she must have known how we loved her; oh that she could now know how deeply, how tenderly we do still & shall ever love her dear joyous face. Blessings on her.—

I could pull many, many other examples. That Darwin had  “emotions” is not a surprise worth a headline. Maybe the BBC is buying into the old cliche that scientists are detached, hyperrational robots. But they should know better.

Whales: big enough, too big, or bigger than big?

This picture can’t do them justice. No picture can.

That’s because this is a picture of a blue whale, the largest animal to live on this planet. Ever.

Goodness knows, people try to show you the size. They put up mounts of blue whale skeletons in museums, or life sized models. There’s a very cool online animation that shows images from the blue whale full sized, on your computer screen, as has it drift by lazily. But I suspect that even these clever things can’t do the trick of conveying what the size of the living, breathing animal must be.

But while the blue whale has the undisputed title of being the biggest, whales, dolphins, and their brethren in general are all very big compared to most mammals. In a new paper, Clauset tests a model that tries to explain why whales might so big.

Normally, when I think of limits to size, I think of biomechanical and physical constraints. “In a big animal, can you make the bone thick enough to move without breaking?”, for instance. This is a common sort of explanation for why you can’t make giant insects like in the old 1950s monster movies:

Strength increases as you make muscles bigger, but strength doesn’t increase as fast as mass does.

What’s interesting about Clauset’s approach is that he explains the sizes of whales without using too many of these sorts of arguments. He does invoke the physics to explain the limits to small sizes. Mammals (and birds) can only be so small because of how they regulate their body temperature. If you’re too small, you cannot eat enough food to make up for the heat flow away from your body.

This thermoregulation problem explains why there are no cat-sized dolphins that you keep in a backyard pool, or hamster-sized porpoises you can keep in a home aquarium. The smallest cetacean is the La Plata dolphin, which are around 35-50 kg as adults. Although the babies are pretty squee-worthy:

Clauset ignores all the details of biomechanical and physical and energetic limitations by rolling all that into “extinction risk.” Can make bones strong enough? Can’t eat enough food? All of those mean that those big species are more likely to go extinct.

Clauset assumes a species can either get bigger or smaller over evolutionary time, although Clauset assumes there are some fitness advantages to being bigger. You have a hard limit on how small you can get set by your ability to themoregulate. The limit to how big you can get is a soft limit set by the likelihood your lineage will go extinct. With only these facts, Clauset’s model fits the size distribution of cetaceans extremely well. Presumably, the same model could be used for terrestrial mammals or birds.

Even the massive blue whale, Clauset says, is not particularly unlikely according to his model. Clauset draws out the line from his model and suggests that it might be possible to have a whale species that is over three times bigger than blue whales; 3.7 times, to be exact. Clauset notes that such a massive whale could not just be the blue whale scaled up. To be bigger than the blues, a new whale species might have to evolve some innovation that would allow them to forage more efficiently than the blue whale’s lunge feeding.

The notion that even the blue what could be dwarfed by another sea creature is an awe inspiring thought.

Reference

Clauset A. 2013. How large should whales be? PLOS ONE 8(1): e53967. DOI: 10.1371/journal.pone.0053967

Blue whale photo by Seabass London on Flickr; used under a Creative Commons license. La Plata dolphin from Washington Post.

Prime times for survival

How long can an insect live? Cicadas might be up near the top. Some cicadas are famous for remaining in the larval stage for thirteen and seventeen years/ That makes them a pretty long lived insect, even if they spend most of that time as larvae underground, out of sight.

A lot of cicadas are synced up in these thirteen and seventeen year cycles, so that in peak years, huge numbers of these insects emerge. Then they are everywhere, singing to attract mates so they can get the next brood of baby cicadas on their long road to maturity.

Now, these two times – thirteen and seventeen years – are notable because they are both prime numbers. As I understood it, the leading explanation is that lots of things in nature tend to cycle. But most of those cycles are fairly short. One possible advantage of something that cycles with a prime number is that it’s unlikely that any other short cyclic events will consistently coincide with the emergence of the new adult cicadas.

Imagine cicadas emerged on a twelve year cycle. Any predator that was on a roughly two, three, four, or six year cycle could sync up with the food feat of cicada emergence – provided there was a little give in their cycles so they could line up in the first place. But that sort of synchronization between predators and prey is much harder to do with a prime number. Thus, cicadas never face large numbers of predators just waiting for them to come out from their long larval stage.

A new paper suggests that the cicadas might even reap a bigger advantage than that.

Koenig and Liebhold do a new analysis estimating how many birds are during each year when cicadas emerge in large numbers, and how many birds when the cicadas don’t. They have population estimates for fifteen predatory bird species over 45 years. Their data set is as old as I am.

Surprisingly, there are routinely fewer birds on the years when cicadas emerge. The authors propose that this indicates that the long cycle has somehow allowed the cicadas to emerge during years that are safer than usual.

The authors do briefly mention alternative hypotheses. Cicadas are famously loud insects. Maybe the cicadas are so abundant and noisy that they actually drive birds away from their normal habitats. They authors say this is unlikely, because the bird counts go down even in places where the cicadas are not calling.

Koenig and Liebhold suggest that it's more or less coincidence that the cicada broods last for a prime number of years. They suggest that the emergence of these huge numbers of insects has some sort of knock-on effects, such that when they occur, the bird populations are effects, and go through booms and busts of their own - and the birds' low point comes around again in about thirteen or seventeen years.

The details of how this might happen aren't clear.

I suppose that the good news about being a cicada researcher is you have time to plan new studies. The bad new is that it probably doesn't take thirteen years to plan those projects... or seventeen years

Reference

Koenig WD, Liebhold AM. 2012. Avian predation pressure as a potential driver of periodical cicada cycle length. The American Naturalist: in press. DOI: 10.1086/668596

Photo by fmerenda on Flickr; used a Creative Commons license.

Why are insects so small now?

Bugs used to be bigger. Much bigger.

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

Picture from here.

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

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

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.

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:

The denial manual

Yesterday, my productivity was way down, because I was watching the Science Writing in the Age of Denial and the Experimental Biology conferences unfold on Twitter. Thanks to all who have been tweeting from them!

I was particularly interested in this “denial manual,” discussed by Sean B. Carroll in the former conference. It was taken from chiropractic attacks on vaccines, but you can see the exact same playbook at work in evolution, global warming, and so on.

1. Doubt the science.
2. Question scientists’ motives and integrity.
3. Emphasize disagreements.
4. Exaggerate potential harm of a position. For example, blame Nazis and WWII on acceptance of evolution.
5. Appeal to personal freedom. For example, use phrases like, “Nothing should be compulsory,” “teach balace,” “allow opt-out.
6. Argue that accepting the conclusions this would invalidate some key personal philosophy.

And that last one is the biggie. Evidence will only matter to someone who hasn’t dug in on that last point.

And, as if to demonstrate, a few climate change denialists found the #sciencedenial and #denialconf hashtags on Twitter. Among the first words they typed were accusations of some of those at the conference being liars and idiots – neatly showing how Point #2 above works.

Similarly, one hashtag got flooded with automated porn spambots. The switch to a second hashtag was seen as evidence of those at the conference not wanting to listen to arguments and “paranoia,” rather than not wanting to wade through irrelevant, automated tweets linking to pornography.

To get a glimpse of Point #5 in action, have a listen to Marc Morano on The Science Show. Morano says to Anna Rose (co-founder of the Australian Youth Climate Coalition):

You are the face of one of the greatest threats of our liberty, and that is intellectual, international bean-counters trying to control average people's lives because they think they know better how people should live, because people left to their own devices will somehow destroy the planet.

If you don't want to listen to Morano, you should listen to Ben Goldacre later in the clip, who has a memorable description of how frustrated he is with the climate debate.

A Storify of the first part of the Science Denial meeting can be found here and here.

Additional: Interesting. The Twitter stream for #denialconf was subject to another attack by porn bots today, at about the same time of day as yesterday. It certainly looks like a deliberate attack on the conference stream, not just happenstance.

As for whether yesterday’s switch to a new hashtag was refusal to engage, here’s a screen grab from today to give an idea of the level of tweets that led to the switch. Click to enlarge.

More additional: A nice blog post about where credibility comes from.

Red is sexy but not sexual

The Methods section of most papers is the least read part of the paper. You can see this in how some journals print the Methods in a tiny point size. Others have taken to putting the section at the end of the paper, so as not to disrupt the narrative flow with details.

Occasionally, you get a paper – usually in your field – where you need to read the Methods section closely to understand a paper enough to criticize or replicate.

Rare indeed are papers where the story is so unusual that I think, “I have absolutely got to read that Methods section!”

A new paper by Johns and colleague marks the first time I thought, “I have to read those Methods,” and “These Methods should come with an NSFW warning.”

It’s about the colour red.

Red seems to affect us in a way that other colours don’t (Elliot et al. 2007, Hill & Barton 2005). Case in point:

These head-turning dresses would not be the show-stoppers they are if they were beige.

Red is sexy.

If that picture doesn’t convincing you, check out Elliot and Niesta, 2008 and go through the data to your heart’s content.

Johns and colleagues test an hypothesis for why red on women looks so attractive to me. The hypothesis is that red is sexy because it reminds men of... lady parts.

An obvious objection to this idea is that t external sex organs of women are not red in the way that the dresses above are red. The hypothesis is a more subtle, however. One version of the hypothesis is that as females are approaching ovulation, the vulva becomes more red than is is at other points in the cycle.

If this “red is code for female sex organs” hypothesis is true, you might predict that men would judge female genitals as more attractive as they became more red.

The Methods section does not disappoint.

Explicit images of anatomically normal, un-retouched, nonpornographic, similarly-orientated female genitals were surprisingly difficult to obtain... We selected photographs that ... did not contain other, potentially distracting, objects (fingers, sex toys, piercings etc.) and were hairless to account for current fashion.

Ah, scientific prose, you’re at your most amusing when you’re trying to act coy.

They showed their pictures to 40 males. Most of the men were in their 20s, and they asked the participants about factors like their sexual orientation (they all reported themselves to be straight) and number of sexual partners. The men rated the attractiveness of each image.

The ratings of attractiveness were the exact opposite of those predicted by the signalling hypothesis. The reddest images were rated the least attractive.

The authors are then tasked to come up with an hypothesis as to why redness is less attractive. Their suggestion is that red is suggestive of menstrual blood. I'm not sure how one would test this hypothesis.

The results also showed that there was no difference in the judgments of men depending on their sexual experience. I learned from the Methods section of this paper that... shhhh, don’t spread this around... one can find pictures of female genitalia on the Internet. Is is possible that the men in this study knew this and might have looked at pictures of ladybits before participating in the study? I know, it’s incredibly unlikely, am I right? But if they did, it might explain why they found no difference in attractiveness ratings according to number of partners the men had.

This study is useful in that it tries to test an adaptive hypothesis experimentally. But it is frustrating because it is a limited study and hard to interpret.

First, there were few stimuli used. Only four pictures were used (then coloured four shades of red, for a total of 16).

Second, and more importantly, for an hypothesis that is all about sex, the authors seemed determined to make everything as clinical and detached and, well, unsexy as possible. First, the pictures were substantially cropped. They didn’t show the labia minora or the clitoris. (Correction; see comments.) As mentioned in the quote above, they didn’t want to use images had any sort of sexual nature (non-pornographic). The female equivalent of this task might have been to evaluate penises for attractiveness from pictures that only showed a flaccid member.

Perhaps not surprisingly, the men didn’t find images of lady parts alone to be very attractive. On a scale of 1 to 100, the average was around 40, except for the reddest, which was rated 35.

I’m curious as to whether the authors would expect to see the same effect with homosexual women.

Finally, there is a great opportunity for further research. The authors note:

Surprisingly little is known about the range of variation in morphology and colour of the external genitalia of normal women of reproductive age, however, and further research is necessary in this area.

I think this could be the chance for someone (not me) to create the best citizen science project ever. “Ladies, all you need to contribute to science is privacy and a camera.” We need data!

Additional: Another take at The View from Helicon.

Reference

Changizi MA, Zhang Q, Shimojo S. 2006. Bare skin, blood and the evolution of primate colour vision. Biology Letters 2(2): 217-221. http://dx.doi.org/10.1098/rsbl.2006.0440

Elliot AJ, Maier MA, Moller AC, Friedman R, Meinhardt J. 2007. Color and psychological functioning: The effect of red on performance attainment. Journal of Experimental Psychology: General 136(1): 154-168.

Elliot AJ, Niesta D. 2008. Romantic red: Red enhances men’s attraction to women. Journal of Personality and Social Psychology 95(5): 1150-1164.

Hill RA, Barton RA. 2005. Psychology: Red enhances human performance in contests. Nature 435(7040): 293-293. http://dx.doi.org/10.1038/435293a

Johns SE, Hargrave LA, Newton-Fisher NE. 2012. Red is not a proxy signal for female genitalia in humans. PLoS ONE 7(4): e34669. 10.1371/journal.pone.0034669

This article is made possible thanks to Helen Lewis, who compiled covers of book on female sexuality for New Statesman.

How Pompeii worms take the heat

This is the Pompeii worm (Alvinella pompejana), and it is a record-holding animal.

Its record is not for the most unlikely animal (though you have to admit, it is a bit odd looking). You are looking at the animal that is able to withstand higher temperatures than anything else in the animal kingdom. The Pompeii worm routinely withstands scalding 80°C water. Not only that, it can routinely go outside of that to water that is more like room temperature, at 20°C.

That this worm is able to take high temperatures makes sense when you consider where these animals live. These are one of the deep sea vent animals that live near water hot enough to melt lead. As I described recently, the animals themselves don’t venture into the superheated water, but stray close enough that temperature is a consideration for them. And when they move away from the water erupting from the bottom of the ocean floor, they can face temperatures that are only a few degrees above freezing.

Most organisms cannot go into temperatures that high, because their proteins, including all the vital enzymes that catalyze almost every reaction in every cell, should be coming apart at the seams. Proteins are long, strand-like molecules, and they work because that strand is folded into complicated shapes. Those shapes are held together by a whole bunch of complex chemical bonds. But high temperatures can break chemical bonds. You see this process in action every time you cook an egg: the high temperatures break the chemical bonds holding the proteins in their particular shapes, and you get new shapes with different properties. This is why eggs go from runny and clear to more solid and white.

A new paper, authored by Jollivet and team, tries to work out just how the proteins in the Pompeii worm are able to hold together in conditions that would turn ours all sproggly (that's the technical term). They do this by a lot of molecular biology to look at the structure of the proteins in the worms en masse. They note two things.

First, the proteins in the Pompeii worm do not like to dissolve in water (hydrophobic). I don’t pretend to exactly understand how that stabilizes the protein, but it seems to be a trend that is also seen in bacteria that thrive in hot springs and the like.

Second, the proteins in the Pompeii worm have a lot of ionized bits. This made a little more intuitive sense to me, as I could imagine how having lots of positive and negative charges in the proteins would allow for the formation of more ionic bonds (salt bridges) along the length of the protein. More bonds within the protein should mean more stability. Ionic bonds are reasonably strong (weaker than covalent bonds, stronger than hydrogen bonds and Van der Waals forces).

The authors take this analysis one step further, and look not only at the Pompeii worm, but a relative (Paralvinella grasslei; alas, it seems to have no common English name), which is nowhere near as tolerant of those high temperatures. Jollivert and company found that many of the changes they saw were not unique to the Pompeii worm; P. grasslei showed some of the same trends. Both worms seemed to have a trend to hydrophobic proteins compared to other species. The authors suggest that the common ancestor of the two may have been more like the Pompeii worm in liking hot water, and that Paralvinella grasslei migrated back into cooler waters during its evolution.

Hot worm. Cool science.

Reference

Jollivet D, Mary J, Gagnière N, Tanguy A, Fontanillas E, Boutet I, Hourdez S, Segurens B, Weissenbach J, Poch O, Lecompte O. 2012. Proteome adaptation to high temperatures in the ectothermic hydrothermal vent Pompeii worm. PLoS ONE 7(2): e31150. DOI: 10.1371/journal.pone.0031150

Be eaten, make glowing fish poo, profit!

Why glow if you don’t have eyes to see?

Glowing takes energy. Down in the deep ocean, energy is in short supply, so why would bacteria do this? Bacteria don’t have eyes. It’s not like they’re going to be able to use it to find stuff. And these bacteria are not living in another organism, so it’s not as though they’re glowing in some sort of mutual trade with a host.

These bacteria only glow when they’re in large numbers, close together (quorum sensing), however. This gives a clue to what might being going on. A new paper by Zarubin and colleagues conducts several experiments to test the hypothesis that these deep sea bacteria are glowing because they want to be eaten.

You might think getting eaten is not a productive thing to do. The idea is: bacteria light up when they’re in large enough numbers to signal decent food. The bacteria themselves might not be the food, so much as the article they’re attached to.

The bacteria use the insides of their consumers as a way to disperse themselves throughout the ocean. It’s already been shown that a fairly large number of these glowing bacteria can survive passage through the gut. But that alone doesn’t provide enough a strong test of the hypothesis that the bacteria glow to advertise themselves as bait.

First, the team tested whether animals preferred glowing bacteria by putting two bags in a big tank of predators. One bag contained glowing bacteria; another contained same species, but with a mutation that prevented the glowing. Decapod and mysid crustaceans went almost all for the glowing bacteria. But it’s not a universal attractor; copepod crustaceans ignored both bags of bacteria.

Brine shrimp (Artemia) would start to glow after swimming in these bacteria, and their guts started to glow after the shrimp ate the bacteria.In the picture below, you can see Artemia in plain light, and after 30 seconds in the dark. The light is dim, but they do indeed glow.

There is a problem here, though: they switched the species eating the bacteria. They don’t say whether they tested if Artemia were attracted preferentially to the glowing bacteria. You can show a plausible chain of events, but to “close the loop” on this story, you’d have to use the same bacteria eaters all the way through. The authors justify this partly by convenience (Artemia are easy to rear in large numbers) and partly by saying that this allows them to see the effect better. Brine shrimp don’t have escape behaviour. Thus, this removed possible confounds of an interaction between the glowing and any movements caused by escape responses. They also say that one of the mysid species glows after contacting the bacteria. They don’t show data for that, or give any citations, however. Their convenience came at the cost of ecological plausibility.

The glowing Artemia are much more likely to be eaten by fish – about ten times more likely. They tested this by putting Artemia in tanks with ring-tailed cardinal fish (Apogon annularis, pictured), which is nocturnal. And after the cardinalfish eat these brine shrimp, the bacteria do fine. They make it all the way through the fish’s digestive system, and they make the resulting feces also glow (though probably not brightly). The authors also tested the feces of other bacteria eaters – the Artemia and mysids – and they also tend to glow.

What I’d like to see next is some indication of whether the zooplankton are getting any nutritional value from eating these bacteria. Are the bacterial consumers being tricked into wasting time consuming “empty calories” that will just pass through their guts without benefit? If so, why haven’t the zooplankton wised up to this? I mean, how embarrassing would it be to be punked by bacteria? Or is these a “selfish herd” sort of situation, where a small proportion of group members are lost, but the risk to individuals is so low? And is there any manipulation of the plankton behaviour by the bacteria, similar to the way large parasites often work?

Reference

Zarubin M, Belkin S, Ionescu M, Genin A. 2012. Bacterial bioluminescence as a lure for marine zooplankton and fish Proceedings of the National Academy of Sciences 109(3): 853-857. DOI: 10.1073/pnas.1116683109

Apogon annularis picture from here.

Once more into the cave

Caves. There’s a whole series of things that tends to happen in creatures that become cave-dwellers. Over and over and over again, animals that live exclusively in caves tend to be blind compared to their closest living relatives.

This makes cave species great for studying evolution, because each cave is a “natural experiment.” Mexican cave fish are a particularly cool case, because we have in the same species both cave dwellers, which are blind, and surface fish, which are not. And they can interbreed.

This new paper looks purely at the genetics of these cave fishes, trying to figure out just how many times they have invaded caves and lost developed the “cave” phenotype. This new paper by Bradic and colleagues is an extensive crunching of gene samples, and concludes that while there were two ancestral populations, those ancestral populations in turn invaded caves several times: a total of five introductions to caves, all told.

Furthermore, although these animals can interbreed in the lab, this seems to be unlikely in nature. Their results indicate low gene flow between the surface population and the cave populations. Still, while low, it’s not zero, suggesting that there is a genuine fitness advantage to the blind cave-dwelling form.

Reference

Bradic M, Beerli P, Garcia-de Leon FJ, Esquivel-Bobadilla S, Borowsky RL. 2012. Gene flow and population structure in the Mexican blind cavefish complex (Astyanax mexicanus). BMC Evolutionary Biology 12: 9. DOI: 10.1186/1471-2148-12-9

Photo by Joachim S. Müller on Flickr; used under a Creative Commons license.

Links

Turning light and going blind: A tale of caves and genes

Males have bigger brains than females, if those males are sticklebacks from Iceland

This supershort paper contains an interesting fact: there is a population of male stickleback fish out there with big brains. The males fish that have brains 23% larger than the females of approximately equal size.

This is a bit of an unfair characterization. The paper does talk a little bit about how the look for differences in brain size according to the local eco-type that they found the fish and: mud or lava. the nails from allow the environments have bigger brains than those from muddy environments, but there is no such difference in the females.

This is an interesting difference, because so few animals have differences in brain size mispronounced between males and females. Kotrschal and colleagues say that this is the biggest difference in overall brain size in males and females to date.

What are we to make of this one interesting fact? The team speculates that this might be because the males make complicated nests, and compete for females through courtship displays. But it seems that there are many other animals that have similar differences in behavior without the differences in overall brain size. Maybe the real question is not why male brains are so big, but why are female brains in this fish so small? The authors speculate that this might be because the females are investing energy in egg production. Again, it doesn’t really answer why it should be so specifically strong in this particular population of this particular fish when all sorts of females invest energy in making eggs.

While the fact that this paper presents is interesting, a fact in isolation is mainly a curiosity, to borrow a phrase from psychologist Ernst Hilgard. I would’ve liked to have seen this fact presented slightly longer paper with a few more experiments and a little more context. There will surely be some interesting follow-up studies to do.

Reference

Kotrschal A, Räsänen K, Kristjánsson B, Senn M, Kolm N. 2012. Extreme sexual brain size dimorphism in sticklebacks: a consequence of the cognitive challenges of sex and parenting? PLoS ONE 7(1): e30055. DOI: 10.1371/journal.pone.0030055

Photo by Noel Burkhead on Flickr; used under a Creative Commons license.

Hidden potential, and the concept of syngeny

There’s much excitement about a new paper in Science that shows how ants have hidden potential. In short, there are a few species of ants that can produce “supersoldiers”. Other ant species, however, can also make supersoliders when they are experimentally give the right dose of hormone.

Crudely, it looks like the ants’ ancestors had the ability by changing the hormone levels, but the pathway that was sensitive to the hormone remained. When species started to evolve differences in hormone levels again, the supersoldier body type “re-emerged” after a long period of suppression.

Ed Yong covers it here and here. One of the authors talks about it on Quirks & Quarks.

I wanted to talk not about the paper so much as a concept it illustrates that I don’t think has gotten enough attention in the evolutionary biology literature.

Homology is a critical concept in evolutionary biology. A generally used definition is a feature that two different species share because they inherited it from a common ancestor. But homology can be tricky, because a “feature” or “trait” isn’t a single thing. Features have different levels of organization: genes, cells, tissues, organs, and so on. And each level can evolve long a different path than the others.

Plus, the concept of homology was first proposed first by Richard Owen, who rejected the idea of evolution by natural selection. And it was widely used before we had learned a lot about the subtleties of genetics.

For instance, we’ve learned that just because you have a gene doesn’t mean it’s expressed. Much like the supersoldier ants, you can imagine a scenario where a gene (or gene network, etc.) is present in an ancestral species, but not expressed. The species diversifies, and diversified, leaving many daughter species with the unexpressed genes. Then, independently, several of the daughters of the original ancestor start expressing the genes, and the trait pops up in distantly related species.

From the point of view of the phylogeny, that feature doesn’t look homologous, even though there is evolutionary continuity at the genetic level from a common ancestor.

Butler and Saidel recognized this scenario some time ago. They coined the term “syngeny” to describe a feature arising from genes that are present, but rarely expressed. I heard Butler discuss this at a J.B. Johnston Club meeting, citing a particular fish brain structure that appears only in a few, not closely related, species. The idea was great.

What the ant story brings that they didn’t have at the time was the ability to bring their feature back through an experimental manipulation. It’s likely that many cases of syngeny are not going to be as easy to show in the lab as in the ants.

Rajakumar and colleagues, the authors on the ant paper, call what they’re seeing parallel evolution, but syngeny might be a better description.

References

Butler A & Saidel W. 2000. Defining sameness: historical, biological, and generative homology BioEssays 22(9): 846-853. DOI: 10.1002/1521-1878(200009)22:93.0.CO;2-R

Rajakumar R, San Mauro D, Dijkstra MB, Huang MH, Wheeler DE, Hiou-Tim F, Khila A, Cournoyea M, Abouheif E. 2012. Ancestral developmental potential facilitates parallel evolution in ants. Science 335(6064): 79-82. http://dx.doi.org/10.1126/science.1211451

Picture by SouthernAnts on Flickr; used under a Creative Commons license.

Calling Nemo

Everyone knows clownfish are pretty. Almost everyone knows they live among the tentacles of anemones. But I’m willing to bet fewer people know that clownfish are noisy.

Fishes make noises for the same sorts of reasons that other animals make noise. Sometimes, it’s to say, “This is what species I am!” Sometimes, it’s to say, “Listen to how big I am!” All kinds of important signals can be contained in sounds. Such behaviours can become important drivers in evolution. Certain kinds of sounds might be considered “sexy” in different groups, and start driving differences in mate choice, and ultimately speciation.

The team of Colleye and colleagues listened to 14 different species of clownfish, most of which were in the genus Amphiprion (A. ocellaris and A. frenatus are shown here). They predicted that if these sound signals were important in the evolution of this group of fishes, they should see lots of diversification in the signals, and not much overlap between them.

This turned out not to be the case. The sounds were quite similar, perhaps because clownfish all make sounds by snapping their jaws together. 

The sounds clownfish make are excellent signals of fish size. Big fish make longer and lower sounding pulses in their calls than small fish. The correlations are tighter than most that you see in biology. (The r values are 0.98 and -0.99! See here for more on correlations.)

This doesn’t support the idea that the sounds are important as way to isolate different species, except incidentally if the species differ in size.

But these signals could be critical to the dynamics between individuals within a group a clownfish, because breeding in groups is dependent on size. If you are the biggest clownfish in your group, you are a reproductive female. If you are the second biggest fish in your group, you are a reproductive male. If you are the third biggest fish in your group... you are a male who doesn’t get to reproduce until one of of the top two go missing. (Yes, clownfish undergo sex changes.)

When your reproductive success depends on size, being able to recognize the information about size in other group members could be critical.

Reference

Colleye O, Vandewalle P, Lanterbecq D, Lecchini D, & Parmentier E. 2011. Interspecific variation of calls in clownfishes: degree of similarity in closely related species BMC Evolutionary Biology 11(1): 365. DOI: 10.1186/1471-2148-11-365

Amphiprion ocellaris by Joachim S. Müller on Flickr; Amphiprion frenatus by brian.gratwicke on Flickr; both used under a Creative Commons license.

New attacks on evolution: throw another one

I make a brief cameo appearance in this LiveScience article about several new anti-evolution bills in state legislatures; specifically, one in New Hampshire.

The bill, House bill 1457, is kind of sad, because it is such a weak attack on evolution. It doesn’t mention evolution, even though the representative who introduced it admits he had it crafted with evolution and intelligent design in mind. The phrase “no matter how firmly it appears to be established” is an admission that anti-evolutionists can’t win on the evidence. They’re just throwing marshmallows now.

Or possibly snowballs.

Only effective in getting the wrong kind of attention.

Photo from here.