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Rhythms of Life in Meatspace and Cyberland
Coturnix
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- December 25, 2011
- 05:59 PM
- 212 views
Evolutionary Medicine: Does reindeer have a circadian stop-watch instead of a clock?
by Bora Zivkovic in A Blog Around The Clock
I originally posted this on April 13th, 2010. Whenever I read a paper from Karl-Arne Stokkan’s lab, and I have read every one of them, no matter how dense the scientese language I always start imagining them running around the cold, dark Arctic, wielding enormous butterfly nets, looking for and catching reindeer (or ptarmigans, whichever [...]
... Read more »
Lu, W., Meng, Q., Tyler, N., Stokkan, K., & Loudon, A. (2010) A Circadian Clock Is Not Required in an Arctic Mammal. Current Biology, 20(6), 533-537. DOI: 10.1016/j.cub.2010.01.042
- August 19, 2010
- 11:22 PM
- 618 views
Food goes through a rabbit twice. Think what that means!
by Bora Zivkovic (coturnix) in A Blog Around The Clock
Coprophagy in rabbits and its circadian control.... Read more »
Bellier R, Gidenne T, Vernay M, & Colin M. (1995) In vivo study of circadian variations of the cecal fermentation pattern in postweaned and adult rabbits. Journal of animal science, 73(1), 128-35. PMID: 7601725
Kenagy, G., & Hoyt, D. (1979) Reingestion of feces in rodents and its daily rhythmicity. Oecologia, 44(3), 403-409. DOI: 10.1007/BF00545245
Kenagy GJ, Veloso C, & Bozinovic F. (1999) Daily rhythms of food intake and feces reingestion in the degu, an herbivorous Chilean rodent: optimizing digestion through coprophagy. Physiological and biochemical zoology : PBZ, 72(1), 78-86. PMID: 9882606
Hörnicke H, Ruoff G, Vogt B, Clauss W, & Ehrlein HJ. (1984) Phase relationship of the circadian rhythms of feed intake, caecal motility and production of soft and hard faeces in domestic rabbits. Laboratory animals, 18(2), 169-72. PMID: 6748594
Pairet M, Bouyssou T, & Ruckebusch Y. (1986) Colonic formation of soft feces in rabbits: a role for endogenous prostaglandins. The American journal of physiology, 250(3 Pt 1). PMID: 3456721
Hörnicke, H., Batsch, F., & Hornicke, H. (1977) Coecotrophy in Rabbits: A Circadian Function. Journal of Mammalogy, 58(2), 240. DOI: 10.2307/1379586
- August 15, 2010
- 10:15 PM
- 690 views
Postscript to Pittendrigh’s Pet Project – Phototaxis, Photoperiodism and Precise Projectile Parabolas of Pilobolus on Pasture Poop
by Bora Zivkovic (coturnix) in A Blog Around The Clock
Review of literature on how Pilobolus fungus orients itself and shoots its spores into a considerable distance.... Read more »
Bruce, V., Weight, F., & Pittendrigh, C. (1960) Resetting the Sporulation Rhythm in Pilobolus with Short Light Flashes of High Intensity. Science, 131(3402), 728-730. DOI: 10.1126/science.131.3402.728
TRAIL, F., GAFFOOR, I., & VOGEL, S. (2005) Ejection mechanics and trajectory of the ascospores of Gibberella zeae (anamorph Fuarium graminearum). Fungal Genetics and Biology, 42(6), 528-533. DOI: 10.1016/j.fgb.2005.03.008
Fischer, M., Stolze-Rybczynski, J., Cui, Y., & Money, N. (2010) How far and how fast can mushroom spores fly? Physical limits on ballistospore size and discharge distance in the Basidiomycota. Fungal Biology, 114(8), 669-675. DOI: 10.1016/j.funbio.2010.06.002
Roenneberg, T., & Merrow, M. (2001) Seasonality and Photoperiodism in Fungi. Journal of Biological Rhythms, 16(4), 403-414. DOI: 10.1177/074873001129001999
Yafetto, L., Carroll, L., Cui, Y., Davis, D., Fischer, M., Henterly, A., Kessler, J., Kilroy, H., Shidler, J., Stolze-Rybczynski, J.... (2008) The Fastest Flights in Nature: High-Speed Spore Discharge Mechanisms among Fungi. PLoS ONE, 3(9). DOI: 10.1371/journal.pone.0003237
- April 13, 2010
- 02:52 AM
- 1,161 views
Evolutionary Medicine: Does reindeer have a circadian stop-watch instead of a clock?
by Coturnix in A Blog Around The Clock
Whenever I read a paper from Karl-Arne Stokkan's lab, and I have read every one of them, no matter how dense the scientese language I always start imagining them running around the cold, dark Arctic, wielding enormous butterfly nets, looking for and catching reindeer (or ptarmigans, whichever animal the paper is about) to do their research.
If I was not so averse to cold, I'd think this would be the best career in science ever!
It is no surprise that their latest paper - A Circadian Clock Is Not Required in an Arctic Mammal (press release) - was widely covered by the media, both traditional and blogs, See, for example, The Scientist, BBC, Scientific American podcast and Wired Science.
Relevant, or just cool?
It is hard to find a science story that is more obviously in the "that's cool" category, as opposed to the "that's relevant" category. For the background on this debate, please read Ed Yong, David Dobbs, DeLene Beeland, Colin Schultz, and the series of Colin's interviews with Carl Zimmer, Nicola Jones, David Dobbs, Jay Ingram, Ferris Jabr, Ed Yong and Ed Yong again.
I agree, it is a cool story. It is an attention-grabbing, nifty story about charismatic megafauna living in a strange wilderness. I first saw the work from the lab in a poster session at a conference many years ago, and of all the posters I saw that day, it is the reindeer one that I still remember after all these years.
Yet, the coolness of the story should not hide the fact that this research is also very relevant - both to the understanding of evolution and to human medicine. Let me try to explain what they did and why that is much more important than what a quick glance at the headlines may suggest. I did it only part-way a few years ago when I blogged about one of their earlier papers. But let me start with that earlier paper as background, for context.
Rhythms of Behavior
In their 2005 Nature paper (which was really just a tiny subset of a much longer, detailed paper they published elsewhere a couple of years later), Stokkan and colleagues used radiotelemetry to continuously monitor activity of reindeer - when they sleep and when they roam around foraging.
You should remember that up in the Arctic the summer is essentially one single day that lasts several months, while the winter is a continuous night that lasts several months. During these long periods of constant illumination, reindeer did not show rhythms in activity - they moved around and rested in bouts and bursts, at almost unpredictable times of "day". Their circadian rhythms of behavior were gone.
But, during brief periods of spring and fall, during which there are 24-hour light-dark cycles of day and night, the reindeer (on the northern end of the mainland Norway, but not the population living even further north on Svaldbard which remained arrhythmic throughout), showed daily rhythms of activity, suggesting that this species may possess a circadian clock.
Rhythms of Physiology
In a couple of studies, including the latest one, the lab also looked into a physiological rhythm - that of melatonin synthesis and secretion by the pineal gland. Just as in activity rhythms, melatonin concentrations in the blood showed a daily (24-hour) rhythm only during the brief periods of spring and fall. Furthermore, in the latest paper, they kept three reindeer indoors for a couple of days, in light-tight stalls, and exposed them to 2.5-hour-long periods of darkness during the normal light phase of the day. Each such 'dark pulse' resulted in a sharp rise of blood melatonin, followed by just as abrupt elimination of melatonin as soon as the lights went back on.
Rhythms of gene expression
Finally, in this latest paper, they also looked at the expression of two of the core clock genes in fibroblasts kept in vitro (in a dish). Fibroblasts are connective tissue cells found all around the body, probably taken out of reindeer by biopsy. In other mammals, e.g., in rodents, clock genes continue to cycle with a circadian period for a very long time in a dish. Yet, the reindeer fibroblasts, after a couple of very weak oscillations that were roughly in the circadian range, decayed into complete arrhytmicity - the cells were healthy, but their clocks were not ticking any more.
What do these results suggest?
There is something fishy about the reindeer clock. It is not working the same way it does in other mammals studied to date. For example, seals and humans living in the Arctic have normal circadian rhythms of melatonin. Some other animals show daily rhythms in behavior. But in reindeer, rhythms in behavior and melatonin can be seen only if the environment is rhythmic as well. In constant light conditions, it appears that the clock is not working. But, is it? How do we know?
During the long winter night and the long summer day, the behavior of reindeer is not completely random. It is in bouts which show some regularity - these are ultradian rhythms with the period much shorter than 24 hours. If the clock is not working in reindeer, i.e., if there is no clock in this species, then the ultradian rhythms would persist during spring and fall as well. Yet we see circadian rhythms during these seasons - there is an underlying clock there which can be entrained to a 24-hour light-dark cycle.
This argues for the notion that the deer's circadian clock, unless forced into synchrony by a 24 external cycle, undergoes something called frequency demultiplication. The idea is that the underlying cellular clock runs with a 24-hour period but that is sends signals downstream of the clock, triggering phenotypic (observable) events, several times during each cycle. The events happen always at the same phases of the cycle, and are usually happening every 12 or 8 or 6 or 4 or 3 or 2 or 1 hours - the divisors of 24. Likewise, the clock can trigger the event only every other cycle, resulting in a 48-hour period of the observable behavior.
If we forget for a moment the metaphor of the clock and think instead of a Player Piano, it is like the contraption plays the note G several times per cycle, always at the same moments during each cycle, but there is no need to limit each note to appear only once per ... Read more »
Lu, W., Meng, Q., Tyler, N., Stokkan, K., & Loudon, A. (2010) A Circadian Clock Is Not Required in an Arctic Mammal. Current Biology, 20(6), 533-537. DOI: 10.1016/j.cub.2010.01.042
- February 3, 2010
- 02:02 PM
- 1,084 views
My latest scientific paper: Extended Laying Interval of Ultimate Eggs of the Eastern Bluebird
by Coturnix in A Blog Around The Clock
Yes, years after I left the lab, I published a scientific paper. How did that happen?
Back in 2000, I published a paper on the way circadian clock controls the time of day when the eggs are laid in Japanese quail. Several years later, I wrote a blog post about that paper, trying to explain in lay terms what I did, why I did it, what I found, and how it fits into the broader context of this line of research. The paper was a physiology paper, and my blog post also focused on the physiological aspects of it.
But then, I wrote (back in March 2006 - eons ago in Web-time) an additional blog post on one of my old blogs (reposted on this one here, here and here) in which I followed further, thinking about the data in more ecological and evolutionary terms, and proposing hypotheses following from the data that can only be tested in other species out in the wild. As you can see if you click on the links, this post did not receive much commentary.
Then, about a year ago, I received an e-mail out of the blue, from a researcher at the Cornell Ornithology Lab, essentially offering to test one of the hypotheses I outlined in that post. My first reaction was "sure, go ahead, I am happy someone wants to do this, but please cite the blog post as the origin of the hypothesis"... The response was along the lines of "no, no, no - we are thinking about working WITH you on testing this hypothesis". Wow! Sure, of course, I'm game!
They already had preliminary data which they sent to me to take a look. They are coming from an ecological tradition and are very familiar with the ecological literature, some of which they sent to me to read. On the other hand, I am coming from a physiological tradition and am very familiar with that literature, some of which I sent to them to read.
A month or so later, one of them, Caren Cooper, came down to Chapel Hill. We met and, over coffee, spent a couple of hours staring at the data and discussed what it all means. Then we got started at writing the paper.
And now, the paper is out: Caren B. Cooper, Margaret A. Voss, and Bora Zivkovic, Extended Laying Interval of Ultimate Eggs of the Eastern Bluebird, The Condor Nov 2009: Vol. 111, Issue 4, pg(s) 752-755 doi: 10.1525/cond.2009.090061
In this paper - which is really a preliminary pilot study (who knows, we may yet get a grant to do more) - Caren and Margaret set up video cameras on a bunch of nests of Eastern Bluebirds (Sialia sialis). From the tapes they got times when the eggs were laid. The times were approximate. But the analysis gave us exactly the same result when we used the times when the nest was obviously empty before the bird sat on it to lay the egg, the times when the bird first got up to reveal the egg to the camera, and the mid-point between those two times.
I am not aware of anyone ever looking at timing of egg-laying in wild birds out in the field. There is a huge literature on timing of laying in quail and chicken (and some in turkeys) in the laboratory, but none I am aware of in wild birds. Most researchers, when asked when their species lays eggs are surprised at the question and answer something along the lines of "no idea, but we find the eggs when we come to check the nests in the morning, so perhaps over night, or at dawn?" So, this paper is a first in this domain.
What we have shown is that bluebirds, just like chicken and quail, have an S-shaped pattern of egg-laying patterns (see my older post for theory and graphic visualization).
The question is: how does a bird "know" when to stop laying? When is enough enough? When is the clutch (all of the eggs laid in one breeding attempt) complete? Most of ecological literature is focused on energetics: are birds getting hungry, have they depleted some important source of energy, etc.
But the circadian field looks for internal mechanisms. Running a circadian clock takes very little energy. Even when the animals are extremely hungry, the clock keeps ticking with no changes in frequency (if anything, the amplitude gets bigger, implying even more work!). Even when an animal gets very sick and is dying, at the time when many bodily functions start ceasing, the clock works until the very end. Being produced by a molecular feedback loop in which some reactions use and others release energy, and all of this happening in just a small number of brain cells, the clock is very energy efficient and does not require the organism to be healthy and well fed.
What is important in regard to circadian regulation of egg-laying is to understand that female birds have not one, but two circadian clocks. Let's call one of them A and the other one B. Clock A is located in the brain (or retinae or pineal or some combination, depending on the species) and is sensitive to light: it readily entrains to a light-dark cycle. No matter what the intrinsic frequency of the clock may be (as uncovered in constant darkness conditions), it is forced to a frequency of exactly 24 hours by the entraining power of the day/night cycle.
Clock B, on the other hand, is intimately tied to reproduction. It is a result of an interplay between the clock in the brain and neuro-endocrine signals between the brain and the ovary (which may itself house its own part of the clock). Brain clock sends hormonal signals to the ovary. Those signals entrain the ovarian rhythms AND result in ovulation. Ovulation itself produces hormones that signal to the brain clock and entrain it. This feedback loop is in itself The Clock. This clock is light-blind and its intrinsic frequency is not 24 hours - it is around 26-27 hours in both quail and chicken, and almost two days long in turkeys.
These two clocks, A and B, interact with each other. Let's imagine a hypothetical scenario in which clocks A and B are very tightly coupled. The external light-dark cycles that all the birds in the wild are constantly exposed to entrain the clock A to the exactly 24 hours period. Clock B, being tightly coupled to Clock A is then also forced to oscillate with a period of exactly 24 hours. What would that mean to the bird? She would be laying one egg per day, always at exactly the same time of day, every single day of her life: in spring, summer, fall and winter. She'd spend all her resources on making big yolky eggs every day. She would be sitting on a huge pile of eggs throughout her life. She would not be able even to move short-distance to a better nesting ground, let alone prepare and undergo a long-distance migration. Her eggs would be also hatching at the rate of one per day. Thus, she would have progeny of a variety of ages at all times, each age having different requirements for care or abilities to follow the mother around. Some hatchlings would freeze to death in winter, or starve to death at time when the food is scarce. Others would die from predation at times when they are highly visible (in the snow) or just because there are so many of them they cannot all hide under a bush.
An opposite scenario: clocks A and B do not interact with each other at all. In this case, A would be entrained to the 24 hour cycle of night and day. Clock B, being light-blind, would freerun with its own endogenous frequency, i.e., with a period of roughly 26-27 hours. Again, the poor bird would be laying one egg per day all of her life. The only difference is that the eggs would not be laid always at the same time of day, but scattered all over the 24-hour cycle. Both scenarios are obviously maladaptive to the bird.
But, oscillator theory provides a third scenario in which clocks A and B are only loosely coupled. There are phase-relationships between the two clocks when they are coupled: A entrains B. There are phase-relationships when the two are at odds: A inhibits B (and thus no ovulation happens). The phase-relationships are dependent on daylength: when the days are short in winter A inhibits B and no eggs are laid. When the days are very long in the middle of the summer (or in constant light) all phases are permissive to ovulation and the clock B can freerun with its own period of 26-27 hours.
But the interesting phenomenon happens in-between, once the length of the day gets just a little bit longer in spring, in normal breeding season. There is only a narrow zone of phase-relationships in which the two clocks are coupled - outside of that zone, ovulation is inhibited. Thus the clock A starts ticking at the beginning of that zone (e.g., at dawn in some species, at around noon in quail) and ... Read more »
Cooper, C., Voss, M., & Zivkovic, B. (2009) Extended Laying Interval of Ultimate Eggs of the Eastern Bluebird. The Condor, 111(4), 752-755. DOI: 10.1525/cond.2009.090061
- May 28, 2009
- 12:41 PM
- 1,708 views
Yes, Archaea also have circadian clocks!
by Coturnix in A Blog Around The Clock
If you ever glanced at the circadian literature, you have probably encountered the statement that "circadian rhythms are ubiquitous in living systems". In all of my formal and informal writing I qualified that statement somewhat, stating something along the lines of "most organisms living on or near the Earth's surface have circadian rhythms". Why?
In the earliest days of chronobiology, it made sense to do most of the work on readily available organisms: plants, insects, mammals and birds. During the 20th century, thousands of species of animals, fungi, protists and plants - all living on the planet's surface - were tested for the possession of the circadian clock, and one was always found. Hence the "ubiquitous" statement seen in so many papers.
But, as it was later discovered, for some marine organisms moon cycles are more important than day-night cycles so they have evolved lunar clocks in addition or instead of circadian clocks (see sponges and cnidaria, for some examples). In the intertidal zone, the tides are more important for survival than the daily rhythms, so the organisms living there have evolved tidal clocks. Animals that live in caves have lost circadian rhythms, at least in behavioral output (a clock may still be operating underneath, driving metabolic or developmental rhythms). In the polar regions, rhythmicity may be seasonal. In subterranean animals, like Blind Naked mole-rats, most individuals are without rhythms, but young males that leave the colony in order to join another one develop rhythmicity during their adventurous journey. In social insects, only the individuals that go outside the hive to forage exhibit daily rhythms.
How does one figure out if an organism has a clock? You need to pick a good output and a way to continuously monitor it. Then you put the organism in constant conditions of light, temperature, air pressure, sound etc., and monitor the output for many days. If you do the statistics on the data at the end of the experiment and see that there is a periodicity in the data (for at least the first 2-3 days)that is reasonably close to 24 hours (between 16 and 32 hours is usually thought to be the limits), you know that your organism of choice has a circadian clock.
In a related experiment, you expose the organism to an environmental periodicity - usually a light-dark cycle, as it is usually the strongest cue, as the evolution of circadian clocks and light-detecting mechanisms is closely intertwined - to see if the rhythmicity of the organism can be synchronized (entrained) to the environmental cycle, indicating that it is a biological function and not the chance quirk in your data. Without these two experiments providing positive data it does not make sense to do any further investigations into mechanisms of entrainment, anatomical location of the clock or the cellular mechanism of the clock.
The trick is to find a good output to monitor. It is easy for rodents - they will run in running wheels (so will cockroaches). Songbirds will jump from perch to perch. Lizards will walk around the cage and tilt the floor from one side to another. And while behavioral output - the general locomotor activity - is not the most reliable (it is very prone to masking effects, so for instance mice will generally not run in wheels in bright light, while rats will), it is usually the easiest and cheapest to monitor and, in most cases (see an example where it failed, while monitoring body temperature worked) will be sufficient.
But what do you do when the organism does not have a measurable behavioral output, especially one that can be continuously monitored by machines? You start thinking very, very hard. And you come up with an alternative. You may be able to implant radiotransmitters and monitor body temperature. Or you may record vocalizations. Or you may take small blood samples several times per day and assay for something like melatonin.
The technological constrains limited our ability to discover circadian clocks in bacteria until the 1990s. Until then, the existence of such clocks was a mystery (one that everyone in the field was eager to see solved). I have written several posts about the discoveries of clocks in bacteria: Circadian Clocks in Microorganisms, Clocks in Bacteria I: Synechococcus elongatus, Clocks in Bacteria II: Adaptive Function of Clocks in Cyanobacteria, Clocks in Bacteria III: Evolution of Clocks in Cyanobacteria, Clocks in Bacteria IV: Clocks in other bacteria, Clocks in Bacteria V: How about E.coli? The understanding of the way bacterial clocks work (more like a relay or a switch than a clock) made us rethink the clock metaphor we have been using for almost a century.
So it appears that most Eukaryotes have clocks and at least some bacteria have them as well. But the other large group - the Third Domain: Archaea - eluded us thus far. After all, Archaea are notoriously difficult to culture in the laboratory and it took some time to figure out how to keep them alive outside of their natural extreme environments.
Do Archaea have clocks? We did not know. Until now. A couple of weeks ago, PLoS ONE published a paper that is the first to demonstrate the daily rhythms in an Archaeon: Diurnally Entrained Anticipatory Behavior in Archaea by Kenia Whitehead, Min Pan, Ken-ichi Masumura, Richard Bonneau and Nitin S. Baliga. Here is the text of the Abstract:
By sensing changes in one or few environmental factors biological systems can anticipate future changes in multiple factors over a wide range of time scales (daily to seasonal). This anticipatory behavior is important to the fitness of diverse species, and in context of the diurnal cycle it is overall typical of eukaryotes and some photoautotrophic bacteria but is yet to be observed in archaea. Here, we report the first observation of light-dark (LD)-entrained diurnal oscillatory transcription in up to 12% of all genes of a halophilic archaeon Halobacterium salinarum NRC-1. Significantly, the diurnally entrained transcription was observed under constant darkness after removal of the LD stimulus (free-running rhythms). The memory of diurnal entrainment was also associated with the synchronization of oxic and anoxic physiologies to the LD cycle. Our results suggest that under nutrient limited conditions halophilic archaea take advantage of the causal influence of sunlight (via temperature) on O2 diffusivity in a closed hypersaline environment to streamline their physiology and operate oxically during nighttime and anoxically during daytime.
What does that mean? What did they do?
First, they picked a good candidate species - Halobacterium salinarum. Why is it a good candidate? Because it lives near the Earth's surface, in salty lakes and ponds (like this one, in Africa):
Many Archaea live in places where no light ever penetrates: deep inside the rock or ice or the oceanic floor. Some Archaea are exposed to light in cyclical fashion but not a 24-hour cycle - I have written somewhere before that I expect the Archaea living in the waters of the Old Faithful geiser in Yellowstone National Park to have a 45-minute clock instead. But Halobacterium salinarum is exposed to the natural periodicity of the day-night cycle on the surface and is thus a good candidate for an Archaeon that may have evolved a circadian clock. This is how the Halobacterium salinarum look like under the microscope:... Read more »
Whitehead, K., Pan, M., Masumura, K., Bonneau, R., & Baliga, N. (2009) Diurnally Entrained Anticipatory Behavior in Archaea. PLoS ONE, 4(5). DOI: 10.1371/journal.pone.0005485
- May 10, 2009
- 04:18 PM
- 1,772 views
Why social insects do not suffer from ill effects of rotating and night shift work?
by Coturnix in A Blog Around The Clock
Most people are aware that social insects, like honeybees, have three "sexes": queens, drones and workers.
Drones are males. Their only job is to fly out and mate with the queen after which they drop dead.
Female larvae fed 'royal jelly' emerge as queens. After mating, the young queen takes a bunch of workers with her and sets up a new colony. She lives much longer than other bees and spends her life laying gazillions of eggs continuously around the clock, while being fed by workers.
Female larvae not fed the 'royal jelly' emerge as workers.
Workers perform a variety of jobs in the hive. Some are hive-cleaners, some are 'nurses' (they feed the larvae), some are queen's chaperones (they feed the queen), some are guards (they defend the hive and attack potential enemies) and some are foragers (they collect nectar and pollen from flowers and bring it back to the hive).
What most people are not aware of, though, is that there is a regular progression of 'jobs' that each worker bee goes through. The workers rotate through the jobs in an orderly fashion. They all start out doing generalized jobs, e.g., cleaning the hive. Then they move up to doing a more specialized job, for instance being a nurse or taking care of the queen. Later, they become guards, and in the end, when they are older, they become foragers - the terminal phase.
This pattern of behavioral development is called "age polyethism" (poly = many, ethism = expression of behavior), or sometimes "temporal polyethism" (image from BeeSpotter):
This developmental progression in behavior is accompanied by changes in brain structure, patterns of neurotransmitter and hormone synthesis and secretion, and patterns of gene expression in the central nervous system.
Some years ago (as in "more than ten years ago") Gene Robinson and his students started looking at daily patterns of activity in honeybees. The workers in their early stages are doing jobs inside the hive, where it is always dark. They clean the hive, take care of the eggs and pupae, and feed the larvae and the queen around the clock. Each individual bee sometimes works and sometimes sleeps, without any semblance of a 24-hour pattern. Different individuals work and sleep at different, apparently random times. The hive as a whole is thus constantly busy - there is always a large subset of workers performing their duties, day and night.
As they get older, they start doing the jobs, like being guards, that expose them to the outside of the hive, thus to the light-dark and temperature cycles of the outside world.
Finally, the foragers only go out during the daytime and have clear and distinct daily rhythms. Furthermore, the foragers have to consult an internal clock in order to orient towards the Sun in their travels, as well as to be able to communicate the distance and location of flowers to their mates in the hive using the 'waggle dance'. As bees are social insects, it is difficult to keep individuals in isolation for longer periods of time, but it has been done successfully and, in such studies, foragers exhibit both freerunning (in constant darkness) and entrained (in light-dark cycles) circadian rhythms, while younger workers do not.
In the Robinson lab, then PhD student Dan Toma and postdoc Guy Bloch did much of the early and exciting work on figuring out how the rhythmicity develops in individual worker bees as they pass through the procession of 'jobs'.
In an early study, they measured levels of expression of mRNA of the core clock gene Period (Per). The gene was expressed at low levels and no visible daily rhythm in early-stage workers, but at much higher levels and in a circadian fashion in foragers.
As the levels of expression were measured crudely - in entire bee brains - it was impossible at the time to be sure which of the two potential mechanisms were operating: 1) the celluular clock did not work until the bee became a forager, or 2) the cellular clocks were working, but different cells were not synchronized with each other, producing a collectively arrhythmic output: both as measured by gene expression of the entire brain and as measured by behavior of the live bee.
Either way, the study showed correlation: the appearance of the functional circadian clock coincided with other changes in the brain structure, brain chemistry and bee behavior. They could not say at the time what causes what, or even if the syncronicity of changes was purely coincidental. They needed to go beyond correlation and for that they needed to experimentally change the timing to see if various processes can be dissociated or if they are tightly bound to each other.
And there is a clever way to do this! First, they took some hives and removed all the foragers from it. This disrupted the harmony of the division of labor in the hive - too many cleaners and nurses, but nobody is bring the food home. When that happens, the behavioral development of other workers speeds up dramatically - in no time, some nurses and guards develop into foragers. And, lo and behold, the moment they became foragers, they developed rhythms in behavior and rhythms of the Per gene expression in the brain. So, as the development is accelerated, everything about it is accelerated at the same rate: gene expression, brain structure, neurochemistry, and behavioral rhythmicity.
Nice, but then they did something even better. They removed most of the cleaners and nurses from some hives. Again, the balance of the division of labor was disrupted - plenty of food is arriving into the hive but there is not enough bees inside to take care of that food, process it, feed the larvae, etc. What happened then? Well, some of the foragers went back into the hive and started performing the house-keeping duties instead of flying out and about. And, interestingly, their brain structure and chemistry reverted its development to resemble that of cleaners and nurses. They lost behavioral rhythmicity and started working randomly around the clock. And the rhythm of clock-gene expression disappeared as well.
So, genetic, neural, endocrine, circadian and behavioral changes all go together at all times. Social structure of the colony, through the patterns of pheromones present in the hive, affects the gene expression, brain development and function, and behavior of individual bees. Just like the gene expression and behavioral patterns, the patterns of melatonin synthesis and secretion in honeybee brains is low and arrhythmic in young workers and becomes greater and rhythmic in foragers. With the recent sequencing of the honeybee genome, the potential for future research in honeybee chronobiology looks promising and exciting.
But are these findings generalizable or are they specific to honeybees? How about other species of bees or other social insects, like wasps, ants and termites? Are they the same?
Other species of socials insects have been studied in terms of age polyethism as well. The earliest study I am aware of (let me know if there is an older one) studying behavioral rhytmicity in relation to behavioral development was a 2004 Naturwissenschaften paper by Sharma et al. on harvester ants. In that study, different castes of worker ants exhibited different patterns - some were strongly diurnal, some nocturnal, some had strange shifts in period, and some were arrhythmic. Those with rhythms could entrain to light-dark cycles as well as display freerunning rhythms in constant darkness.
Just last month, a new paper on harvester ants came out in BMC Ecology (Open Access). In it, Ingram et al. show that foragers have circadian rhythms (both in constant darkness and entrained to LD cycles) in expression of Period gene (as well as behavioral rhythms), while ants working on tasks inside the hive do not exhibit any rhythms either in clock-gene expression or in behavior, suggesting that the connection between age polyethism and the development of the circadian clock may be a universal property of all social insects.
We know that in humans, night-shift and rotating-shift schedules are bad for health as the body is in the perpetual state of jet-lag:... Read more »
Yang, L., Qin, Y., Li, X., Song, D., & Qi, M. (2007) Brain melatonin content and polyethism in adult workers of Apis mellifera and Apis cerana (Hym., Apidae). Journal of Applied Entomology, 131(9-10), 734-739. DOI: 10.1111/j.1439-0418.2007.01229.x
Sharma, V., Lone, S., Goel, A., & Chandrashekaran, M. (2004) Circadian consequences of social organization in the ant species Camponotus compressus. Naturwissenschaften, 91(8). DOI: 10.1007/s00114-004-0544-6
Ingram, K., Krummey, S., & LeRoux, M. (2009) Expression patterns of a circadian clock gene are associated with age-related polyethism in harvester ants, Pogonomyrmex occidentalis. BMC Ecology, 9(1), 7. DOI: 10.1186/1472-6785-9-7
- April 12, 2009
- 07:38 PM
- 1,788 views
Why eliminate the peer-review of baseline grants?
by Coturnix in A Blog Around The Clock
About a week ago, my brother sent me a couple of interesting papers about funding in science, one in Canada, the other in the UK. I barely had time to skim the abstracts at the time, but thought I would put it up for discussion online and come back to it later. So I posted the link, abstract and brief commentary a few days ago to the article: Cost of the NSERC Science Grant Peer Review System Exceeds the Cost of Giving Every Qualified Researcher a Baseline Grant:
Abstract: Using Natural Science and Engineering Research Council Canada (NSERC) statistics, we show that the $40,000 (Canadian) cost of preparation for a grant application and rejection by peer review in 2007 exceeded that of giving every qualified investigator a direct baseline discovery grant of $30,000 (average grant). This means the Canadian Federal Government could institute direct grants for 100% of qualified applicants for the same money. We anticipate that the net result would be more and better research since more research would be conducted at the critical idea or discovery stage. Control of quality is assured through university hiring, promotion and tenure proceedings, journal reviews of submitted work, and the patent process, whose collective scrutiny far exceeds that of grant peer review. The greater efficiency in use of grant funds and increased innovation with baseline funding would provide a means of achieving the goals of the recent Canadian Value for Money and Accountability Review. We suggest that developing countries could leapfrog ahead by adopting from the start science grant systems that encourage innovation.
A long and interesting discussion ensued in the comments, with the author of the paper himself showing up and offering to send reprints to those who are interested. More discussion also happened on FriendFeed here and here.
Several other bloggers also posted about it, and discussions happened on their posts as well. T. Ryan Gregory posted about it both on his Nature Network blog Pyrenaemata and on his indy blog Genomicron.
Larry Moran was largely in agreement with the article, but some commenters were not, including Rosie Redfield whose comment motivated T. Ryan Gregory to post again, just to explain his disagreement with Rosie.
Jonathan Eisen pointed out to a related post of his and Cameron Neylon to a related post of his. Finally, Zen Faulkes used it as a starting point for three posts here,
here and here.
I have finally managed to find time to read the paper myself so I think I can say something semi-intelligent about it. It became obvious that many who commented have not actually read the paper, just the Abstract, and thus were not in the position to respond to it intelligently (the paper actually answers, clearly and in detail, all the questions and complaints voiced by the commenters). The abstract is just, ...well, an abstract. The paper is full of thought-provoking ideas and really needs to be read in its entirety.
Finally, my brother showed up in the comments and I would like to use his comment as a starting point today. That is - once you read the actual paper (ask for a reprint if you cannot access it), the linked blog posts and comment threads. I'll be right here, waiting for you to come back....
I am assuming that the Canadian funding system is not very dissimilar to that in many other countries, including the USA - there is a central governmental body that gets its budget from the government and uses committees of unpaid peer-reviewers to decide how the money will be allocated to the researchers. The paper explains in detail at least a dozen reasons why and how this system is flawed: how it stifles truly innovative science, repels students from entering science, disproportinately pushes women out of science, encumbers students and postdocs with tasks they are not supposed to be doing (e.g., clerical, or technical), introduces an element of uncertainty about one's livelihood, gives universities excuses to completely get out of research funding, shafts teaching and outreach as criteria for promotion, etc. But the clincher, for politicos at least, is that this system costs more than if a set sum of about $30,000 (Canadian) was given to every academic employed by a Canadian university who asks in any given year.
Yes, giving every Canadian scientist who already has a job and a lab this small amount of money no-questions-asked, geared toward innovative exploratory research, costs the government less than going through the peer-review system that gives money to some and no money to others (not to mention the reinforcement of the Old Boys Club this way).
This does not mean, in their proposal, that all of the Canadian money earmarked for science would be given this way - this is still just a small part of it. If you have a big lab or do expensive research and need to apply for much bigger grants, that would be done by the traditional peer review. But in order to get to the point where you have a good proposal, you need to have some neat stuff done (the "preliminary data"). With the proposed system, that preliminary data can be really exciting or revolutionary, something that, as an initial proposal, would never fly by peers.
Would people send out proposals for crap? Some would, I'm sure, but that doesn't matter. Most would not. Scientists are curious about nature and would like to test their hunches. Some will flop, some will be amazing - it is the latter that this new system is worth doing for, as they may never be done otherwise. Anyway, how many $5,000,000 grants produced amazing stuff? All? I.Don't. Think.So.
Where does quality control come from? First, it already came from universities who hired these researchers out of hundreds of applicants for each position. Aren't they going to trust those best-of-the-best they hired? Second, the research itself will be judged after it is done - at conferences, in journal articles, and in post-publication metrics (citations, downloads, online chatter, etc., including perhaps a Nobel Prize here and there). If it is not up to standards, $30,000 Canadian dollars is not a big price to pay, and even the negative or inconclusive results can be useful to others if the thinking is original. If it is up to standards or more, that person will now have something exciting to base a bigger grant proposal on.
This also goes back to something I like to rant about (oh yes, go read that again!) - the bandwagon of Big Science. Biology, for example, does not equal running gels (hmmm, that's chemistry, isn't it?). But many people are given that appearance. "No gels - no grants, no papers, no career" (yup, I was told that a few years ago). Unless you already have a big molecular lab, this small grant will not build you one. Instead, you can do some really cool stuff at other levels - from tissues up to ecosystems and everything in-between, including computer modeling. You can use it to travel to some jungle that has never seen a Westerner and see what species live there - not hypothesis-testing, exploratory and exciting, definitely useful, but not something that is easily funded with a current system. If your proposal includes research on live vertebrates, you first have to get an IACUC proposal, something that will take 6-9 months of extremely frustrating fighting and proposal-modification - getting an IACUC proposal is the toughest peer-review known to science: if they say Yes to your proposal, no other committee of peers can add any more wisdom to it. And if you decide to work on invertebrates - it is much cheaper.
Another paper looks at this from another perspective - four stages of science. The grants, especially the big ones, disproportionately target science in Stage 3. The small baseline grants would target primarily Stage 1, the exciting, innovative stage - and this is a Good Thing. They could also more easily fund research in Stage 2 and Stage 4, also a Good Thing - from the article:
In this article I propose the classification of the evolutionary stages that a scientific discipline evolves through and the type of scientists that are the most productive at each stage. I believe that each scientific discipline evolves sequentially through four stages. Scientists at stage one introduce new objects and phenomena as subject matter for a new scientific discipline. To do this they have to introduce a new language adequately describing the subject matter. At stage two, scientists develop a toolbox of methods and techniques for the new discipline. Owing to this advancement in methodology, the spectrum of objects and phenomena that fall into the realm of the new science are further understood at this stage. Most of the specific knowledge is generated at the third stage, at which the highest number of original research publications is generated. The majority of third-stage investigation is based on the initial application of new research methods to objects and/or phenomena. The purpose of the fourth stage is to maintain and pass on scientific knowledge generated during the first three stages. Groundbreaking new discoveries are not made at this stage. However, new ways to present scientific information are generated, and crucial revisions are often made of the role of the discipline within the constantly evolving scientific environment. The very nature of each stage determines the optimal psychological type and modus operandi of the scientist operating within it. Thus, it is not only the talent and devotion of scientists that determines whether they are capable of contributing substantially but, rather, whether they have the 'right type' of talent for the chosen scientific discipline at that time. Understanding the four different evolutionary stages of a scientific discipline might be instrumental for many scientists in optimizing their career path, in addition to being useful in assembling scientific teams, precluding conflicts and maximizing productivity. The proposed model of scientific evolution might also be instrumental for society in organizing and managing the scientific process. No public policy aimed at stimulating the scientific process can be equally beneficial for all four stages. Attempts to apply the same criteria to scientists working on scientific disciplines at different stages of their scientific evolution would be stimulating for one and detrimental for another. In addition, researchers operating at a certain stage of scientific evolution might not possess the mindset adequate to evaluate and stimulate a discipline that is at a different evolutionary stage. This could be the reason for suboptimal implementation of otherwise well-conceived scientific policies.
Now, the proposal in this paper is quite definitive about allowing only researchers employed by universities to apply for such grants. But my mind instantly started thinking about those outside. How about amateur scientists? How about people not affiliated with the academia? How about distributed citizen science projects? Those are usually Stage 1 or Stage 2 projects, attractive to a particular kind of researcher (myself included - don't try to lure me into a big Stage 3 lab). If I wanted to get some crayfish or spiders (or even birds, if a local IACUC would let me) and do experiments at home, this kind of a small grant would be just ideal. Could I have a local University, or some peers, write a letter in support of my proposal? Would that fly?
The paper also mentions, in a couple of places, similarities and differences between peer-review of grants and peer-review of manuscripts, including the importance of Openness to science. In one place, it mentions new journals "where ideas may be published initially unreviewed, but anyone may append public discussions to each article". I am hoping this refers to arXiv and Nature Precedings, or even the concept of Open Notebook Science, but it smells too much like one of the pernicious myths spread by the enemies of Open Access about PLoS ONE which is, as readers of this blog are aware, stringently peer-reviewed.
One thing that the article mentions is that the current granting system allows researchers to buy time for research away from their teaching time. They note this as bad for teaching, true, but there is another angle to it. As danah writes in regard to the new proposed NSF funding of qualitative research, this kind of work does not require much in terms of equipment, but much in terms of time. It is essential for people, especially in social sciences, who do qualitative research, to be able to buy the time they need to do their research correctly.
Oh, and I mentioned at the beginning that my brother sent me two papers, yet we talked here only about one of them. The other one, if you are interested in starting a whole new discussion, is this one: Life after death? The Soviet system in British higher education
Recent studies of British higher education (HE) have focused on the application of the principles of the 'new managerialism' in the public sector, ostensibly aimed at improving the effectiveness of research and teaching, and also on the increasing commercialisation of HE. This article examines HE management in the light of the historical experience of the Soviet system of economic planning. Analogies with the dysfunctional effects of the Soviet system are elaborated with regard to financial planning and the systems of quality control in academic research and teaching. It is argued that Soviet-style management systems have paradoxically accompanied the growing market orientation of HE, undermining traditional professional values and alternative models of engagement between HE institutions and the wider society.
A FriendFeed discussion has started. Read the entire paper before chiming in, of course - we are scientists here!
Gordon, R., & Poulin, B. (2009). Cost of the NSERC Science Grant Peer Review System Exceeds the Cost of Giving Every Qualified Researcher a Baseline Grant Accountability in Research, 16 (1), 13-40 DOI: 10.1080/08989620802689821 Read the comments on this post...... Read more »
Gordon, R., & Poulin, B. (2009) Cost of the NSERC Science Grant Peer Review System Exceeds the Cost of Giving Every Qualified Researcher a Baseline Grant. Accountability in Research, 16(1), 13-40. DOI: 10.1080/08989620802689821
- February 4, 2009
- 12:17 AM
- 1,819 views
An Awesome Whale Tale
by Coturnix in A Blog Around The Clock
When I was a little kid, almost nothing was known about evolution of whales. They were huge, they were marine and they were mammals, but their evolutionary ancestry was open to speculation. Some (like Darwin himself) hypothesized that the terrestrial ancestor of whales looked like a bear. Others favored the idea of a hippo-like or even a pig-like ancestor.
Over the decades, two things happened. First, the revolution in molecular biology and computing power allowed scientists to compare many genes of many mammals and thus infer genealogical relationships between whales and other groups of mammals. Second, some smart palaeontologists decided that a good place to look for fossil whales would be Pakistan. The rest is, as they say, history. Digs in Pakistan unearthed a wealth of whale fossils over the years, so many of them, in fact, that the fossil record of prehistoric whales is now one of the best examples of the bushy tree of mammalian evolution in any lineage.
We now know that there were several gradual changes in whales over their evolutionary history from terrestrial animals to a number of branches of aquatic animals - some of these branches went extinct over time, while others have living descendants today. They tended to increase in size. Their front legs evolved into flippers. They gradually lost their hind legs: the large, strong hind legs of early whales were used for swimming by paddling, but later decreased in size as the undulating mode of swimming (and the evolution of the flat horizontal tail) took over. Today's whales have remnants of hind legs still hidden deep inside their large bodies, in the form of two smalish bones.
While genetics discovers evolutionary relationships, and fossils can tell us about evolution of morphology, it is much more rare that a fossil find allows us to infer much about an extinct animal's physiology, behavior or ecology. And the discovery of one such fossil was just published in PLoS ONE today: New Protocetid Whale from the Middle Eocene of Pakistan: Birth on Land, Precocial Development, and Sexual Dimorphism (also watch the accompanying video of the fossil). Here is the abstract:
Background
Protocetidae are middle Eocene (49-37 Ma) archaeocete predators ancestral to later whales. They are found in marine sedimentary rocks, but retain four legs and were not yet fully aquatic. Protocetids have been interpreted as amphibious, feeding in the sea but returning to land to rest.
Methodology/Principal Findings
Two adult skeletons of a new 2.6 meter long protocetid, Maiacetus inuus, are described from the early middle Eocene Habib Rahi Formation of Pakistan. M. inuus differs from contemporary archaic whales in having a fused mandibular symphysis, distinctive astragalus bones in the ankle, and a less hind-limb dominated postcranial skeleton. One adult skeleton is female and bears the skull and partial skeleton of a single large near-term fetus. The fetal skeleton is positioned for head-first delivery, which typifies land mammals but not extant whales, evidence that birth took place on land. The fetal skeleton has permanent first molars well mineralized, which indicates precocial development at birth. Precocial development, with attendant size and mobility, were as critical for survival of a neonate at the land-sea interface in the Eocene as they are today. The second adult skeleton is the most complete known for a protocetid. The vertebral column, preserved in articulation, has 7 cervicals, 13 thoracics, 6 lumbars, 4 sacrals, and 21 caudals. All four limbs are preserved with hands and feet. This adult is 12% larger in linear dimensions than the female skeleton, on average, has canine teeth that are 20% larger, and is interpreted as male. Moderate sexual dimorphism indicates limited male-male competition during breeding, which in turn suggests little aggregation of food or shelter in the environment inhabited by protocetids.
Conclusions/Significance
Discovery of a near-term fetus positioned for head-first delivery provides important evidence that early protocetid whales gave birth on land. This is consistent with skeletal morphology enabling Maiacetus to support its weight on land and corroborates previous ideas that protocetids were amphibious. Specimens this complete are virtual 'Rosetta stones' providing insight into functional capabilities and life history of extinct animals that cannot be gained any other way.
What does this all mean? Unlike the gradual loss of hind legs, graudal increase in size, gradual evolution of front legs into flippers and gradual evolution of the horizontal tail, we did not have information about the way the prehistoric whales gave birth. We know that all large terrestrial mammals give birth head-first, while all aquatic mammals (not just whales, but also manatees and such) give birth tail-first. But we did not know when did this switch occur.
This paper shows that some early whales, already well along the way of evolving into creatures recognizable as whales but still possessing sizeable hind legs they used for swimming, gave birth head-first. This indicates that these animals, at least on those rare occasions when they were giving birth to their young, had to go up onto dry land. Thus, we now have the timing a little better on the question of when exatly did the whales become completely aquatic, i.e., never coming to land at all, and it is somewhat later than we thought until now.
I tried to explain this in as simple language as possible - suitable for complete laymen or middle-school students, but if you want a little more detail and some better expert opinion on this fossil find and the paper that describes it, please read what others have written about it:
Carl Zimmer
Mike Dunford
Ed Yong
Brian Switek
Greg Laden
Cosmos Magazine
WIRED Science
Philip D. Gingerich, Munir ul-Haq, Wighart von Koenigswald, William J. Sanders, B. Holly Smith, Iyad S. Zalmout (2009). New Protocetid Whale from the Middle Eocene of Pakistan: Birth on Land, Precocial Development, and Sexual Dimorphism PLoS ONE, 4 (2) DOI: 10.1371/journal.pone.0004366 Read the comments on this post...... Read more »
Philip D. Gingerich, Munir ul-Haq, Wighart von Koenigswald, William J. Sanders, B. Holly Smith, & Iyad S. Zalmout. (2009) New Protocetid Whale from the Middle Eocene of Pakistan: Birth on Land, Precocial Development, and Sexual Dimorphism. PLoS ONE, 4(2). DOI: 10.1371/journal.pone.0004366
- February 1, 2009
- 04:20 PM
- 1,647 views
Circadian Rhythm of Aggression in Crayfish
by Coturnix in A Blog Around The Clock
Long-time readers of this blog remember that, some years ago, I did a nifty little study on the Influence of Light Cycle on Dominance Status and Aggression in Crayfish. The department has moved to a new building, the crayfish lab is gone, I am out of science, so chances of following up on that study are very low. And what we did was too small even for a Least Publishable Unit, so, in order to have the scientific community aware of our results, I posted them (with agreement from my co-authors) on my blog. So, although I myself am unlikely to continue studying the relationship between the circadian system and the aggressive behavior in crayfish, I am hoping others will.
And a paper just came out on exactly this topic - Circadian Regulation of Agonistic Behavior in Groups of Parthenogenetic Marbled Crayfish, Procambarus sp. by Abud J. Farca Luna, Joaquin I. Hurtado-Zavala, Thomas Reischig and Ralf Heinrich from the Institute for Zoology, University of Gottingen, Germany:
Crustaceans have frequently been used to study the neuroethology of both agonistic behavior and circadian rhythms, but whether their highly stereotyped and quantifiable agonistic activity is controlled by circadian pacemakers has, so far, not been investigated. Isolated marbled crayfish (Procambarus spec.) displayed rhythmic locomotor activity under 12-h light:12-h darkness (LD12:12) and rhythmicity persisted after switching to constant darkness (DD) for 8 days, suggesting the presence of endogenous circadian pacemakers. Isogenetic females of parthenogenetic marbled crayfish displayed all behavioral elements known from agonistic interactions of previously studied decapod species including the formation of hierarchies. Groups of marbled crafish displayed high frequencies of agonistic encounters during the 1st hour of their cohabitation, but with the formation of hierarchies agonistic activities were subsequently reduced to low levels. Group agonistic activity was entrained to periods of exactly 24 h under LD12:12, and peaks of agonistic activity coincided with light-to-dark and dark-to-light transitions. After switching to DD, enhanced agonistic activity was dispersed over periods of 8-to 10-h duration that were centered around the times corresponding with light-to-dark transitions during the preceding 3 days in LD12:12. During 4 days under DD agonistic activity remained rhythmic with an average circadian period of 24.83 ± 1.22 h in all crayfish groups tested. Only the most dominant crayfish that participated in more than half of all agonistic encounters within the group revealed clear endogenous rhythmicity in their agonistic behavior, whereas subordinate individuals, depending on their social rank, initiated only between 19.4% and 0.03% of all encounters in constant darkness and displayed no statistically significant rhythmicity. The results indicate that both locomotion and agonistic social interactions are rhythmic behaviors of marbled crayfish that are controlled by light-entrained endogenous pacemakers.
I think the best way for me to explain what they did in this study is to do a head-to-head comparison between our study and their study - it is striking how the two are complementary! On one hand, there is no overlap in methods at all (so no instance of scooping for sure), yet on the other, both studies came up with similar results, thus strengthening each other's findings. You may want to read my post for the introduction to the topic, as I explain there why studying aggression in crayfish is important and insightful, what was done to date, and what it all means, as well as the standard methodology in the field. So, let's see how the two studies are similar and how the two differ:
1) We were sure we used the Procambarus clarkii species. They are probably not exactly sure what species they had, so they denoted it as Procambarus sp., noting in the Discussion that it was certainly NOT the Procambarus clarkii, which makes sense as our animals were wild-caught in the USA and theirs in Germany. As both studies got similar results, this indicates that this is not a single-species phenomenon, but can be generalizable at least to other crayfish, if not broader to other crustaceans, arhtropods or all invertebrates.
2) We used only males in our study. They used only females. In crayfish, both sexes fight. It is nice, thus, to note that other aspects of the behavior are similar between sexes.
3) We used the term 'aggression'. They use the term 'agonistic behavior', which is scientese for 'aggression', invented to erase any hints of anthropomorphism. Not a bad strategy, generally, as assumed aggression in some other species has been later shown to be something else (e.g., homosexual behavior), but in crayfish it is most certainly aggression: they meet, they display, they fight, and if there is no place to escape, one often kills the other - there is no 'loving' going on there, for sure.
4) The sizes of animals were an order of magnitude different between the two studies. Their crayfish weighed around 1-2g while ours were 20-40g in body mass. This may be due to species differences, but is more likely due to age - they used juveniles while we used adults. Again, it is nice to see that results in different age groups are comparable.
5) We did not measure general locomotor activity of our animals in isolation. We, with proper caveats, used aggressive behavior of paired animals as a proxy for general locomotor activity, and were straightforward about it - we measured aggressive behavior alone in a highly un-natural setup. As Page and Larimer (1972) have done these studies before, we did not feel the need to replicate those with our animals.
The new study, however, did monitor gross locomotor activity of isolated crayfish. Their results, confirming what Page and Larimer found out, demonstrate once again that activity rhythms are a poor marker of the underlying circadian pacemaker (which is why Terry Page later focused on the rhythm of electrical activity of the eye, electroretinogram - ERR - in subsequent studies) in crayfish. Powerful statistics tease out rhythmicity in most individuals, but this is not a rhythm I would use if I wanted to do more complex studies, e.g., analysis of entrainment to exotic LD cycles or to build and interpret a Phase-Response Curve. Just look at their representative example (and you know this is their best):
You can barely make out the rhythm even in the light-dark cycle (white-gray portion of the actograph) and the rhythms in constant darkness (solid gray) are even less well defined - thus only statistical analysis (bottom) can discover rhythms in such records. The stats reveal a peak of activity in the early night and a smaller peak of activity at dawn, similarly to what Page and Larimer found in their study, and similar to what we saw during our experiments.
6) They used an arena of a much larger size than ours. We did it on purpose - we wanted to 'force' the animals to fight as much as possible by putting them in tight quarters where they cannot avoid each other, as we were interested in physiology and wanted it intensified so we could get clearly measurable (if exaggerated) results. Their study is, thus, more ecologically relevant, but one always has to deal with pros and cons in such decisions: more realistic vs. more powerful. They chose realism, we chose power. Together, the two approaches reinforce and complement each other.
7) As I explained in my old post - there are two methodological approaches in this line of research:
Two standard experimental practices are used in the study of aggression in crustaceans. In one, two or more individuals are placed together in an aquarium and left there for a long period of time (days to weeks). After the initial aggressive encounters, the social status of an individual can be deduced from its control of resources, like food, shelter and mates.
In the other paradigm, two individuals are allowed to fight for a brief period of time (less than an hour), after which they are isolated again and re-tested the next day at the same time of day.
They used the first method. We modified the second one (testing repeatedly, every 3 hours over 24 hours, instead of just once a day).
What they did was place 6 individuals in the aquarium, a couple of hours before lights-off, then monitor their aggressive behavior over several days. What they found, similar to us, is that the most intense fights resulting in a stable social hierarchy occur in the early portion of the night:
Once the social hierarchy is established on that first night, the levels of aggression drop significantly, and occasional bouts of fights happen at all times, with perhaps a slight increase at the times of light switches: both off and on. Released into constant darkness, the pattern continues, with the most dominant individual initiating aggressive encounters a little more often during light-transitions then between them. The other five animals had no remaining rhythm of agonistic behavior: they just responded to attacks by the Numero Uno when necessary.
In our study we tried to artificially elevate the levels of aggression by repeatedly re-isolating and re-meeting two animals at a time. And even with that protocol, we saw the most intense fights at early night, and most conclusive fights, i.e., those that resulted in stable social hierarchy, also occuring at early nights, while the activity at other time of the day or night were much lower.
8) The goals of two studies differed as well, i.e., we asked somewhat different questions.
Our study was designed to provide some background answers that would tell us if a particular hypothesis is worth testing: winning a fight elevates serotonin in the nervous system; elevated serotonin correlated with the hightened aggression in subsequent fights, more likely leading to subsequent victories; crayfish signal dominance status to each other via urine; melatonin is a metabolic product of serotonin; melatonin is produced only during the night with a very sharp and high peak at the beginning of the night; if there is more serotonin in the nervous system, there should be more melatonin in the urine; perhaps melatonin may be the signature molecule in the urine indicating social status.
In order to see if this line of thinking is worth pursuing, we needed to see, first, if the most aggressive bouts happen in the early night and if the most decisive fights (those that lead to stable hiararchy) happen in the early night. This is what we found, indicating that our hypothesis is worth testing in the future.
They asked a different set of questions:
Is there a circadian rhythm of locomotor activity? They found: Yes.
Is there a circadian rhythm of aggression? They found: Yes.
Do the patterns of general activity and aggressive activity correlate with each other? They found: Yes.
Does the aggression rhythm persist in constant darkness conditions? They found: Yes.
Do all individuals show circadian rhythm of aggression? They found: No. Only the most dominant individual does. The others just defend themselves when attacked.
Is there social entrainment in crayfish, i.e., do they entrain their rhythms to each other in constant conditions? They found: No. All of them just keep following their own inherent circadian periods and drift apart after a while.
Is there a pattern of temporal competitive exclusion, i.e., do submissive individuals shift their activity patterns so as not to have to meet The Badassest One? They found: No. All of them just keep following their own inherent circadian periods.
So, a nice study overall, the first publication I know of that attempts to connect the literature on circadian rhythms in crayfish to the literature on aggressive behavior in crayfish.
Except.... Read the rest of this post... | Read the comments on this post...... Read more »
A. J. Farca Luna, J. I. Hurtado-Zavala, T. Reischig, & R. Heinrich. (2009) Circadian Regulation of Agonistic Behavior in Groups of Parthenogenetic Marbled Crayfish, Procambarus sp. Journal of Biological Rhythms, 24(1), 64-72. DOI: 10.1177/0748730408328933
- December 20, 2008
- 12:00 PM
- 1,755 views
Einstein was smart, but Could He Play the Violin? - the winner of the synchroblogging contest
by Coturnix in A Blog Around The Clock
Happy Anniversary, PLoS ONE!
Today is PLoS ONE's second anniversary and we're celebrating by announcing that the winner of the second PLoS synchroblogging competition is SciCurious of the Neurotopia 2.0 blog.
"This fluent post captures the essence of the research and accurately communicates it in a style that resonates with both the scientific and lay community" - Liz Allen, PLoS.
Here is the winning entry, cross posted in its entirety:
====================
Einstein was smart, but Could He Play the Violin?
I already wrote one entry for PLoS ONE's second birthday, but I'm feeling sparky today, and I think I like this paper better.
I don't know about you guys, but when I was a sprog, my parents dragged me to music lessons. LOTS of music lessons. As of right now, I have been producing music of some type for the past 21 years straight. And I LOVE it.
Of course, I didn't always love it. I remember my mother dragging me and my brother to lessons, making us sit down every day and practice (I was, and still am, no good with the practicing), and the fear and shakiness of recitals (heck, I still get that, and it's been 21 years). In her time, Sci has actually "mastered" (it's a debatable point), three different instruments ('instruments' is a loose term), and still uses one of them professionally on occasion. And if you can guess what they are, Sci will...do something cool. Like send you one of her favorite books. Or perhaps a tshirt with a molecule on it. Or perhaps some of her delicious cookies. Obviously, you can only guess if you don't KNOW already (that means you, Dad). So there you go, contest open.
Anyway, years and years of music lessons. But the question is: did they do me any good? Does playing 'Baby Mozart' really do anything, and is anything achieved by starting your child on Suzuki when they are 2, other than the pain and misery of your child, and possibly an eventual love of music? Can it, perhaps, make me SMARTER?
Forgeard et al. "Practicing a musical instrument in childhood is associated with enhanced verbal ability and nonverbal reasoning" PLoS ONE, 2008.
And for the record, Einstein did play the violin. Apparently he was quite good.
There actually are several studies out there that show that techniques that you learn can "transfer" to other techniques, giving you a bit of an edge. This works best when you're performing skills that are very similar to each other (like learning how to estimate the area of a square, and then learning how to estimate the area of a triangle). We know this happens for musicians in the development of fine motor skills. Once you've been playing the violin for a while, other things that require fine motor skills will come to you a bit easier (perhaps we should train all would-be surgeons on musical instruments, if you can master playing Rachmaninoff, brain surgery should be a piece of cake).
Of course, most of the studies that have been done are correlational in nature. Kids who play musical instruments have better motor skills. This could be due to the music, or the kids could play music because they have good motor skills. Good motor skills could be a development of things like the higher socio-economic class that often goes along with being taught music as a child, and thus parents are maybe able to put more effort to their development. The possibilities go on. Correlation is NOT causation.
The same thing goes for the correlation between musical learning and IQ. There was a modest correlation, but it could be just the effect of the extra lessons the kids were receiving, resulting in more time spent on focused attention and mastering a skill. Significant correlations have also been shown for music and verbal and language skills. Music lessons have been found to be correlated with increases in reading ability and phonetic comprehension. This actually leads me to a question: if language, reading, and phonetic comprehension are related to the pitch and tone of words, do children who are tone deaf have a harder time mastering reading and verbal skills? I think this might warrant a future PubMed search.
Unfortunately, all the previous tests tended to focus on the "transfer" of skills to not very related fields, like IQ. So in this study, the authors wanted to look at the effects of music learning on "near" transfers, skill closely related to music training: spatial reasoning, verbal abilities, nonverbal, and mathematical. They also looked for VERY closely related skills: fine motor control and auditory skill.
They grabbed a whole bunch of kids around 8-11 years old. Some played musical instruments, some didn't (one of the problems with this study to me is that the control group is a good bit small than the instrumental group, 41 musicians vs 18 non). Kids were controlled for the socio-economic class of the parents. Average length of music training was close to five years. They also divided the kids up by whether or not they got Suzuki training, but ended up grouping them together, as Suzuki effects were no different from other instrumentalists.
Dang, they didn't graph their data. Well, I shall fix. Because I can. People should be so grateful I do all their graphing...
There you go. So, as you can see from the graph (the pretty, pretty graph), musical kids scored a lot better on fine motor skills for left and right hand (the first two sets of bars). This is pretty expected, if you're using fine motor skills a lot, presumably you'll get better at them. The musical kids also did better when distinguishing tones and following melody lines, though interestingly, they didn't show any improvements in rhythm. I wonder if this has anything to do with the kids of music the kids were studying. There wasn't a single drummer in the bunch, it was all either piano or stringed instruments.
And finally, the kids with musical training scored a lot better (I know it doesn't look like it, but the MANCOVA analysis uncovered a difference) on vocabulary testing. They outperformed their non-musical counterparts in both verbal ability (vocabulary) and non-verbal reasoning skills. They didn't find any differences in math or spatial reasoning.
The authors hypothesize that music training may transfer skills to some other related domains. The other hypothesis is that music training doesn't enhance a specific skill set, but rather your general intellectual ability. This would mean they would score higher on every test given. In fact, they DID score higher, but most of the time the scores didn't reach significance.
Still, remember this is correlation, not causation. Families were of similar socio-ecoomic class and education, but that doesn't mean they are all similar parents. Kids who take music lessons may have parents that are more involved in their intellectual development. Kids that persist in taking music lessons for a good chunk of time may have superior motivation. Correlation =/= causation.
But it's still a cool paper, and no matter what, it's quite clear that music lessons didn't HURT. Time to tape your poor child to the piano bench!
Marie Forgeard, Ellen Winner, Andrea Norton, Gottfried Schlaug (2008). Practicing a Musical Instrument in Childhood is Associated with Enhanced Verbal Ability and Nonverbal Reasoning PLoS ONE, 3 (10) DOI: 10.1371/journal.pone.0003566 Read the comments on this post...... Read more »
Marie Forgeard, Ellen Winner, Andrea Norton, & Gottfried Schlaug. (2008) Practicing a Musical Instrument in Childhood is Associated with Enhanced Verbal Ability and Nonverbal Reasoning. PLoS ONE, 3(10). DOI: 10.1371/journal.pone.0003566
- October 5, 2008
- 07:47 PM
- 1,269 views
Wikipedia, just like an Organism: clock genes wiki pages
by Coturnix in A Blog Around The Clock
The October issue of the Journal of Biological Rhythms came in late last week - the only scientific journal I get in hard-copy these days. Along with several other interesting articles, one that immediately drew my attention was Clock Gene Wikis Available: Join the 'Long Tail' by John B. Hogenesch and Andrew I. Su (J Biol Rhythms 2008 23: 456-457.), especially since John Hogenesh and I talked about it in May at the SRBR meeting.
Now some of you may be quick to make a connection between this article and its author Andrew Su and A Gene Wiki for Community Annotation of Gene Function, published in PLoS Biology back in July, where one of the authors is also Andrew Su. And you would be right - it's the same person and the two articles are quite related.
In the PLoS Biology article, they write:
A loose organization of Wikipedia editors has spearheaded the creation and expansion of several thousand articles related to molecular and cellular biology (the "MCB Wikiproject"), including many gene-specific pages. These articles vary widely in quality, format, and completeness, ranging from relatively complete encyclopedic entries (e.g., "enzyme," "oxidative phosphorylation," and "RNA interference") to very short collections of information called "stubs" (e.g., "amphinase" and "glomus cell"). As an example of the collaborative writing process, the article on RNAi has been edited 708 times by 232 unique editors since its initial creation in October 2002. On the subject of human genes, generally only the most well-characterized of genes and proteins have highly developed entries (e.g., "HSP90" and "NF- B").
In principle, a comprehensive gene wiki could have naturally evolved out of the existing Wikipedia framework, and as described above, the beginnings of this process were already underway. However, we hypothesized that growth could be greatly accelerated by systematic creation of gene page stubs, each of which would contain a basal level of gene annotation harvested from authoritative sources. Here we describe an effort to automatically create such a foundation for a comprehensive gene wiki. Moreover, we demonstrate that this effort has begun the positive-feedback loop between readers, contributors, and page utility, which will promote its long-term success.
In the JBR paper, the authors focus on the development of Wikipedia pages describing genes involved in circadian rhythms, probably the first genes to be done comprehensively there, as an example for others as to how to do this kind of thing:
Why use Wikipedia for this? First, Google and Wikipedia have already become scientific research tools. When you Google an unfamiliar gene you usually end up at common sites of gene annotation such as the National Center for Biotechnology Information. Though these sites have expert curators who do the best they can, they are usually not domain experts and are so overloaded that they frequently fall behind in accurately summarizing the literature. (It's actually amazing what they accomplish given available resources.) For confirmation, research your favorite gene. Using Wikipedia will allow our community to build and evolve living, up-to-date summaries on the function of important genes in the circadian network. Check out the pages on Arntl (http://en.wikipedia.org/wiki/ARNTL) and Rev-erb-alpha (http://en.wikipedia.org/wiki/Rev-ErbA_alpha). Second, in part due to Wikipedia's past success, its pages appear near the top of search engine lists such as Google, and consequently attract viewers. Finally, our field competes with other disciplines for the best and the brightest young scientists. These people use Wikipedia. High quality pages on annotated clock genes will attract their attention, and attract them to our field.
Importantly, the gene pages need not be extremely long. What is much more important is that they be well referenced. See, for instance Wikipedia pages they mention, those for ARNTL gene (also known as Bmal1 or Mop3), or Rev-ErbA alpha (I have written about some of these genes before, e.g., Lithium, Circadian Clocks and Bipolar Disorder, Tau Mutation in Context and The Lark-Mouse and the Prometheus-Mouse if you want more background). That is all that is needed - if I wanted to be silly, I could say that since genes are small, their wiki pages need to be small as well. But that is only half-silly, really.
This is just like in the real world. Genes don't really do anything. They are coded descriptions of parts in a catalog. To explain a biological function, one needs to go from genes to their mRNAs to proteins, then to look at protein modifications and how multiple proteins interact with each other. Then see how such protein interactions affect the behavior of a cell. Then see how the altered behavior of a cell affects the entire tissue and how the changes in that tissue affect distant organs. Finally, one gets to explain the function once one understands how a collection of organs, interacting with the external environment, results in changes in biochemistry, development, physiology or behavior of the organism, and how this function evolved.
In the same way, gene pages on Wikipedia are not supposed to be stand-alone. Knowing everything about a clock gene does not mean one knows anything about circadian rhythm generation and modulation (not to mention its evolution). The value is in links - to all the other clock genes, to genes that do similar things (e.g., other transcription factors or nuclear receptors), to primary literature on the proteins coded by these genes and their interactions, and to higher-level functions, e.g., the Circadian Rhythms page and links within.
Some would ask - Why Wikipedia (I know, there are still some people out there who don't like it):
What's the downside? The major criticism is poor annotation. Actually, we argue that no annotation is worse than poor annotation, as the latter tends towards self-correction by provoking experts to intervene. In fact, a recent study concluded that Wikipedia was as accurate as Encyclopedia Britannica, and unlike Britannica, growing at a rate of 1500 articles per day (Giles, 2006). Another potential downside is non-consensual or controversial entries. We would argue that these are better addressed in real time via Wikipedia than in journal articles, where they remain fixed for years. Wikipedia even has tools to deal with controversial topics (for examples, see entries on "Intelligent Design," evolution, "Swift-boating," or climate change).
And, I'd argue, clock gene pages are not as contentious as those on climate change or creationism. Very few Wikipedia pages are so controversial as to be continuously suspect. Almost all of the pages are on non-controversial subjects, written and edited by experts on the topic, and are as reliable, or better, as anything else one can find out there, not to mention the fastest to get updated once new information comes in.
The effort is starting with the focus on mammalian genes, for obvious reasons of medical relevance and the existence of a wealth of information. But there is just as much, if not more, information on Drosophila clock genes. And comparative analysis of clock-genes in a variety of organisms is the key to understanding the circadian function and its evolution, so if your strength is in other old or emerging model organisms (did you see Japanese quail on that list?!), don't hesitate to add the pages and information on those.
Finally, I'd like to urge you to contribute - I know that many chronobiologists read this blog (though most are silent types who never comment). It will take 30-60 minutes of your time to make or edit a page on the gene (or a higher-level process) in circadian biology and this effort will have much bigger audience and much broader impact than all of your peer-reviewed papers put together. It's worth your time even if probably will have no effect on your getting tenure. But the tenure committee is not your only audience - there are researchers around the world (many in developing countries), teachers and students and lay audience, who will be affected by your contribution in a much more lasting and important ways than the inner circle of your department. Isn't this why you are doing science in the first place?
If you want to discuss this more, come to ScienceOnline09, where John Hogenesh, one of the authors of the JBR article, will demonstrate Wiki Genes, answer questions, and deeply internalize your suggestions ;-)
References:
John B. Hogenesch and Andrew I. Su, Clock Gene Wikis Available: Join the 'Long Tail', J Biol Rhythms 2008 23: 456-457.
Jon W. Huss, Camilo Orozco, James Goodale, Chunlei Wu, Serge Batalov, Tim J. Vickers, Faramarz Valafar, Andrew I. Su (2008). A Gene Wiki for Community Annotation of Gene Function PLoS Biology, 6 (7) DOI: 10.1371/journal.pbio.0060175 Read the comments on this post...... Read more »
Jon W. Huss, Camilo Orozco, James Goodale, Chunlei Wu, Serge Batalov, Tim J. Vickers, Faramarz Valafar, & Andrew I. Su. (2008) A Gene Wiki for Community Annotation of Gene Function. PLoS Biology, 6(7). DOI: 10.1371/journal.pbio.0060175
- June 25, 2008
- 10:01 PM
- 1,792 views
Why do earthworms come up to the surface after the rain?
by Coturnix in A Blog Around The Clock
Believe it or not, this appears to have something to do with their circadian rhythms!
Back in the 1960s and early 1970s, there was quite a lot of research published on the circadian rhythms in earthworms, mostly by Miriam Bennett. As far as I can tell, nobody's followed up on that work since. I know, from a trusted source, that earthworms will not run in running-wheels, believe it or not! The wheels were modified to contain a groove down the middle (so that the worm can go only in one direction and not off the wheel), the groove was covered with filter paper (to prevent the worm ... Read more »
Shu-Chun Chuang, & Jiun Chen. (2008) Role of diurnal rhythm of oxygen consumption in emergence from soil at night after heavy rain by earthworms. Invertebrate Biology, 127(1), 80-86. DOI: 10.1111/j.1744-7410.2007.00117.x
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