You may think that the image is a photoshop, or a drawing, or that perhaps the LEGO model does exist somewhere, perhaps in some studio in Japan, or at ITER construction site itself.

But no. The model is in the middle of the Scientific American newsroom! A couple of weeks ago when I went to our New York City office, I took these photos of the model. Now that the embargo has lifted, I can show you some more details of the model:

You can read the article she wrote from that interview on her blog (also re-published on The SA Incubator itself).

Below is the full “transcript” of what I told Erin – I thought some of you may find it interesting:

1. Scientific American’s blog network is extensive. Why have a blog dedicated specifically to the work of young science journalists?

There are several reasons for it. Let me try to cover all the main points.

Limit on the network size.

Scientific American’s blog network is relatively big as networks go, but still limited in size for a number of reasons. There is a limited budget, for starters.

Second, a network any larger than this would be a strain on time and effort for me and developers to manage. At this point, it is at least possible for an interested reader to read all the posts on the network (I do!). If it gets any bigger, this becomes impossible and the readers’ habits change: instead of at least occasionally checking out all the bloggers they only focus on their favorites (some readers always will, but at least some don’t) – thus the ‘network effect’ for bloggers is diminished.

Finally, a blog network is not a simple, additive collection of writers – it is a community of people who work together, write together, read each other, comment on each other’s posts, coordinate their blogging, socialize in the backforums (and in real life when opportunities arise through travel), help each other as needed, etc. If the network gets too big, this feeling of belonging to a “family” evaporates, and there is even a danger of the community splitting into warring factions.

It is important for a network to have a mix of seasoned bloggers and fresh voices on the network, for a variety of reasons (for example, veterans serve as role-models, cheerleaders, advisers and troll-beaters for the newbies). While it is important for the network to have as much diversity as possible, so each blogger can tap into and bring in a different audience, it is also important for the community to be coherent and friendly so one blogger’s audience also checks out the other bloggers.

As a natural rotation occurs – some bloggers leave and new ones get invited in their place – both the diversity and coherence need to stay in place. That would be impossible to pull off if the network was too large. We have space for perhaps 2-3 more blogs to reach that maximum.

Being left out.

When there is a limit on the network’s size, this means new people cannot easily get in. And there may be many of them and quite deserving of spotlight. Many of the youngest writers are still in school, too busy with class assignments, or are in internships, or are too busy breaking into freelancing to be able to blog with regular frequency. Some of them do most or all of their writing in more traditional venues, for pay, and do not have blogging experience at all. Some may want to write but do not want to blog. I don’t want to force them to do what they cannot or will not do, yet feel I should highlight their work elsewhere anyway.

Thus SA Incubator interviews and linkfests. And thus open invitation to young writers to submit pitches for the Guest Blog.

Push vs pull media.

Writers and journalists who specialize in science, health and envirionmental reporting tend to write for specialized news outlets – science magazines, New York Times Science every Tuesday, NPR Science Friday, science cable channels, science blogs – places that are easy to avoid if one is not interested in science. They have the requisite background (often in science as well as journalism), training and knowledge to do it right. But they tend to be hired to write for outlets mostly visited by audiences who actively seek science content – that is the “pull” method. Readers pulled into specialized science media tend to already have sufficient background and interest in science.

How do we reach the unsuspecting audiences, those that do not actively seek science content? How do we grab and bring in people who don’t even know that science is fun? They may be looking for politics, or celebrity gossip, or sports, not science. How do we “push” science on them, show them it is fun, important and relevant for them?

One way is for each one of us to push the science stories to our non-sciency friends on social networks (Twitter, Facebook, Google Plus, etc). But even better method is by having cool science stories appear in outlets where they congregate – the “mass” media outlets, from New York Times to Huffington Post, to public radio, to cable TV, to Hollywood.

Specialized vs. mass media.

Unfortunately, science stories in the mass media tend not to be written by specialized science writers, and are thus often wrong. I do not intend to pick specifically on Larry Moran but this link to his blog I have handy and is fresh in my mind – his is just a recent example of a very frequently seen category error – blaming bad mass media reporting on science journalists. Larry saw a really bad science story on the cover of USA Today and blamed it on science journalists. The problem is: that story was not written by a science journalist! There is nothing science journalists (e.g., NASW members) can do about it – it is not in their power to “police” people who are not part of their cohort.

Vast proportion of science stories in mass media are not written by science journalists. They are written by beat reporters who are required to turn in, let’s say, 7 articles per day (that is an hour of research and writing for each) only tiny proportion of which have anything to do with science. They do not have the background, expertise and experience in science reporting to get it right. They are not given sufficient time to do the research necessary to get it right. They are incapable of accessing, reading and understanding a jargony scientific paper (or even know they are supposed to at least try to read it) in order to get it right. So they submit bad copy. And their editors, not knowing anything about science reporting either, run with it.

Shaming the MSM (Main-Stream Media).

Much of what science bloggers do – and do very well – is critique the science coverage by the mass media. They fisk the bad articles, often several per day, sometimes as systematically as going line by line to show where the articles got the science wrong. This is actually a great educational method – by showing how and why each sentence is wrong, it allows the science blogger to teach the readers the correct version of science in question, as well as how to think critically about science coverage.

Believe me – the authors of these articles and their editors know when this happens to them. Their knee-jerk response is to get very defensive and dismissive (“dirty, hippy bloggers covered by cheeto dust, blogging in their pyjamas in their parents’ basements” is the stereotype they may use or imply), but they get burned and subconsciously learn the lesson to be more careful and at least not repeat the same mistakes in the future.

If a particular mass media outlet (Daily Mail comes to mind) consistently publishes bad science articles, and gets snarkily yet devastatingly criticized for it by knowledgeable expert bloggers almost every day, there is only so long they can remain dismissive of those criticisms. They may not publicly say anything, but they will think, and they will have internal meetings discussing what to do to improve their science coverage as to avoid future criticism.

If this happens, and if they have sufficient budget, the obvious solution is to hire a specialist science reporter. Where do you find one? Google it. What do you find? Hopefully, Scientific American, its articles written by freelancers, its blogs, its weekly Scienceblogging linkfests, or ScienceOnline interviews, or amazing posts on the Guest Blog, or the interviews and weekly linkfests on The SA Incubator. Hire away! Let the good young writers infiltrate the media giants and transform them from within.

Friends in Low Places.

I tell all the young, upcoming science writers to carefully read every word of the transcript of the commencement speech to Berkeley Journalism School’s Class of 2011 given by Robert Krulwich after his mind-blowing experience at ScienceOnline2011. Friends in Low Places. Helping each other. Going Places. Becoming a New Paradigm.

I am one of those. I started blogging on a whim, back in 2004. I got invited to a blog network early on – in 2006. I got a job in the comments section of my blog post in 2007. I got my current job in 2010 because of my blogging. This is a success story.

I never had the Impostor Syndrome when I was doing research. I still have Impostor Syndrome as a writer. English is my second language. I was not trained to write. I don’t know how to turn a pretty phrase. I know nothing about structure and composition of an article. I have difficulty writing on deadline. Why would anyone want to read what I write – my over-long, convoluted, stream-of-consciousness blog posts? I don’t know!

But obviously some people do. And they became my community, my second family. It is that community that helped me every step of the way. They cheered me on. They hit my PayPal button when I was jobless. They pushed for me to get hired. They keep coming to ScienceOnline, they hug me at tweetups, they submit posts to Open Laboratory, they say Yes when I invite them to join the SciAm blog network, they were there for me all along and helped me climb over that wall that Krulwich talks about.

It’s payback time. It is now my turn to help others climb that wall, too.

It was easier to get noticed back when I started. Veteran bloggers or veteran science writers do not need much promotion. But there are many great new voices in the science writing world. This world is now big and growing fast, so it is getting harder and harder to get heard over the din. I find it my duty to seek out and hear those voices, discover talent, promote them, help them climb over the wall.

I’ve been doing it all along – nothing makes me happier than when someone I discovered, encouraged and promoted “makes it” in the real world, gets recognition, hopefully a paid gig! That’s what I see as my main mission in life. I guess that’s why they call me the Blogfather.

Horizontal loyalty.

This is another phrase from the Krulwich’s talk:

So for this age, for your time, I want you to just think about this: Think about NOT waiting your turn.

Instead, think about getting together with friends that you admire, or envy. Think about entrepeneuring. Think about NOT waiting for a company to call you up. Think about not giving your heart to a bunch of adults you don’t know. Think about horizontal loyalty. Think about turning to people you already know, who are your friends, or friends of their friends and making something that makes sense to you together, that is as beautiful or as true as you can make it.

And when it comes to security, to protection, your friends may take better care of you than CBS took care of Charles Kuralt in the end. In every career, your job is to make and tell stories, of course. You will build a body of work, but you will also build a body of affection, with the people you’ve helped who’ve helped you back.

This is really the key reason why I started The SA Incubator. And why I invite young writers to write for the Guest Blog. And why we always try to get ample travel grants for students to attend ScienceOnline. And why I always (not successfully yet) submit a “young writers” panel for the NASW and WCSJ and AAAS meetings.

It is not so much about helping new writers get jobs in old media companies (though that helps pay bills for a little while). It is about helping them find each other, build relationships, build friendships, build start-ups, build a whole new science writing ecosystem that will automatically do both “push” and “pull” and reach everyone and displace bad science reporting from the most visible areas of the media, while providing them with a living. This requires a lot of them, but they need to know each other and work together toward that goal. The SA Incubator is one of those “meeting places” for them. And Khalil and I are planning some features in the future that will make this aspect even more visible.

2. In general, how does the blog do in terms of activity (comments, hits, etc) compared to others in the Scientific American network?

Unlike most of the other blogs on the network, The SA Incubator had to start from zero. No old subscribers to bring on over from “the old blog”. No fascinating blogger author to lure his or her fans. And no clear and obvious clue at the outset what the blog was going to be about. It also did not get all of the needed attention at the beginning as I had to focus on bigger priorities in getting the network built, launched, started and promoted.

It took some time to figure out how the blog should really look like – and certainly to make it clearer to the readers what to expect there if they keep coming back. But over the last few weeks, as the frequency of posting has increased, as Khalil Cassimally joined me as a co-blogger, and already profiled writers spread the links to the interviews around their own networks, I can see that the traffic is starting to grow quite nicely. Too early to tell, though.

What is more important than the immediate traffic to each post is the longevity – Scientific American has, as you can expect, quite a lot of “google juice”, so future searches for the names of writers should bring one to the Incubator interviews. I see it more as a lasting repository than as a source of daily hits gone viral.

3. When deciding to profile a journalist or include their work in the Incubator, what qualities or characteristics are you looking for? If someone wanted to be included how should they go about that?

This first period of interviews is, naturally, populated by people whose work I am already very familiar with. I may have even met them in person, e.g., at Science Writers or ScienceOnline conferences, local tweetups etc. I have followed their work for a year or two and I like what they do. Perhaps they pitched me a story or two for the Guest Blog. Or I may be a regular reader of their personal science blogs.

As a Visiting Faculty at the NYU program for science, health and environmental reporting, and a member of the advisory board of the equivalent UNC program, I am familiar with students from these two schools. And I also try to familarize myself with the work of students at other schools as much as I can.

As the series progresses, Khalil and I will need to get familiar with the work of others, perhaps new people just coming into the field.

There are many ways to do that – follow/subscribe/friend us on Twitter, Facebook, Google Plus and elsewhere. Become a regular commenter on our network’s blogs (yes, I read all the comments). Pitch me a story for the Guest Blog. Email us a little introduction to yourself. When you write a good blog post, or make a video, podcast or infographic, or have an article published somewhere, let me know – just DM me the link on Twitter. If I like it, I will promote it. If I like your stuff in general, I am likely to ask you for a SA Incubator interview as well.

Daily cycle of light and darkness in the environment is a selective factor – having an internal clock is an adaptation that allows organisms to predict and prepare for instead of passively react to cyclical changes in the environment. The regularity of the light-dark cycle is usually a good predictor for other (perhaps not as precise) cycles of temperature, availability of food, or activity of predators.

It gets trickier for organisms that live in places where the light-dark cycle may be missing for big chunks of the year (the polar regions), or where light-dark cycle is not a good predictor of other relevant events in the environment (e.g,. cannot predict rain in very arid regions), or where light cannot penetrate at all (deep ocean, caves, underground burrows). In such organisms the clock may get uncoupled from some of its functions, e.g., it may still time biochemical but not behavioral events. Or the clock may be temporarily or permanently turned off.

Even animals that constantly live in caves still tend to have functioning circadian clocks even if they are not used by these animals to drive rhythms in behavior. In animals that regularly travel into and out of the caves, like bats, the clock is robust.

A number of organisms have been studied in which the clock may temporarily be turned off. In the chestnut tree , circadian clock stops in winter. In reindeer in the high Northern latitudes, behavioral rhythms (and underlying clock) work only during the short springs and autumns, not during the long polar winters and summers. In social insects, castes that spend their time inside the hive and need to work around the clock also do not have a functioning circadian clock.

The organisms that live in extreme environments tend to be difficult to study. It may be a harsh environment for the human researchers to spend long periods of time in. The organisms may not be easy to bring into the lab to study under controlled conditions. Most of such organisms are far from being standard “laboratory models” which means that little is known about their genetics, biochemistry, physiology and behavior.

Thus, one is limited in choices as to which rhythms to study and what conclusions one can take from such studies. A limited number of overt rhythms can be easily monitored in a standardized manner even in the laboratory. A record of overall physical activity and movement is usually made. Additional measured rhythms may be daily fluctuations in hormones, e.g., melatonin. And tissue samples may be taken over a 24-hour period for analysis of patterns of expression of core clock genes.

This approach may miss stuff. For example, even if there is no cycling of clock genes or overt behavioral rhythms, this does not mean that the clock may not be working anyway – cytoplasmatic cellular clocks, or ensembles of neural cells producing weak rhythms, or hormonal feedback loops between endocrine glands could still be producing daily cycles in some aspects of metabolism not identified by the researchers. The adaptive function of the clock is so strong, if nothing else for coordinating internal events, that is is difficult to persuasively and definitively demonstrate that absolutely nothing in the body cycles around a 24-hours cycle.

An important function of the clock is also in measuring changes in daylength – days get longer in spring and shorter during fall. Even environments that have no daily cycles for a while, or no utility in using light-dark cycles, may have strong seasonality, and seasons are another important aspect of the environment related to time. Most organisms use their circadian clocks to measure the changes in daylength through a mechanism called photoperiodism. So even organisms that have no use for daily clocks, may still retain them for their higher-level function of fine-tuning the annual calendar of events.

Domestication also has an effect on circadian clock as one can argue that the lab and the farm are “extreme environments” in some sense. It is well known that many domesticated strains of laboratory mice, rats and nematodes have lost seasonality. Most of our domesticated animals have vastly prolonged breeding seasons – sometimes spanning the entire year, or adding a Fall season to the existing Spring one  – compared to their wild relatives. Domestication may be a strong selective force for abandoning seasonality, which reduces the need for a functional circadian clock as well, especially if human care – feeding, defense, etc. – replace the need for the organism to fend for itself in sync with the cycles of nature.

Now a new player is entering this line of research – barley (Hordeum vulgare). Last week, Faure et al, published an open access paper in PNAS showing that strains of barley from Northern Europe have mutations in one of their photoperiodic genes – EARLY MATURITY8 (EAM8) – and that this gene greatly reduces the amplitude of expression of the core circadian clock genes.

As a result, northern varieties of barley can start flowering early and fast in the season, completely ignoring daylength, just following the normal developmental program. At the same time the disrupted clock allows for much longer daily activity of photosynthesis during long summer days, as it does not shut it down before darkness arrives in the evening.

One can imagine how such mutants were prized in the earlier history of the domestication. As humans moved more and more north, only the barley that could be harvested early and produced large yields was valuable. Late harvest may have been too late: humans may have already moved on, driven by hunger, and left the field to be harvested by birds. Or the harvest, being so small and late, would have been used only for consumption (winter is coming – time to brew some beer!) and not for seed for the next year.

Plant circadian clocks are very complex at the molecular level, involving several different feedback loops in expression, some operating in the morning, others in the evening, etc. Importantly, some of the genes involved in photoperiodism and flowering are intricately connected to the clock and may be a part of some of the clock feedback loops. Most of the past research focused on the way clock genes regulate flowering genes. This is an unusual paper in that it discovers the opposite direction – how a gene involved in flowering feeds back on the clock genes and regulates the way the clock works.

What is exciting about this work is that barley is not a difficult organism to do research on. One does not need heroic efforts or expensive Arctic or speleological gear to study it – it is a domesticated plant, easily grown in fields, glasshouses and labs. Furthermore, much of its biology is already well known, including the similarity between its genes and those of Arabidopsis thaliana, the standard model for plant research.

As a number of strains of barley exist, some southern some northern, there is plenty of material to do comparative studies to figure out exactly which genes and processes were involved in the process of domestication – what was selected for as the humans took their crops with them on their northward migrations. This makes barley potentially a useful standard laboratory model for the general studies of evolution under domestication.

Reference:

Faure, S., Turner, A.S., Gruszka, D., Christodoulou, V., Davis, S.J., von Korff, M. & Laurie, D.A. Mutation at the circadian clock gene EARLY MATURITY 8 adapts domesticated barley (Hordeum vulgare) to short growing seasons, Proceedings of the National Academy of Sciences, DOI: 10.1073/pnas.1120496109

Related at Scientific American:

Chestnut Tree Circadian Clock Stops In Winter
Evolutionary Medicine: Does reindeer have a circadian stop-watch instead of a clock?
Domestication – it’s a matter of time (always is for me, that’s my ‘hammer’ for all nails)
Why social insects do not suffer from ill effects of rotating and night shift work?
Clock Evolution
Whence Clocks?
Circadian clock without DNA–History and the power of metaphor
Basics: Biological Clock
Clock Classics: It All Started with the Plants

Image: Wikimedia Commons, public domain.

Since this article came out in The American Scientist in early 1999 (you can read the entire thing here (pdf)) I have read it many times, I used it in teaching, I discussed it in Journal Clubs, and it is a never-ending fascination for me.

Back in the 1950s, Dmitri Konstantinovich Belyaev started an experiment in which he selectively bred Silver Foxes, very carefully, ONLY for their tameness (and “tameness” was defined very rigorously in terms of type and speed of response, distance that triggers aggression, etc.).

What happened really fast in this experiment is that many other traits showed up, seemingly out of nowhere, in the subsequent generations. They started having splotched and piebald coloration of their coats, floppy ears, white tips of their tails and paws. Their body proportions changed. They started barking. They improved on their performance in cognitive experiments. They started breeding earlier in spring, and many of them started breeding twice a year.

Most of the people reacting to this experiment invoked pleiotropy, i.e., how changes in one gene affect expression of many other genes. See this NYT article for instance. However, even while I was reading it for the first time, my mind screamed – development!

And not just development, but more specifically, heterochrony – change in timing of developmental event.

If you alter the expression of one of the genes that affects developmental timing, you affect all sorts of things.

For instance, when the neural crest cells migrate they become melanocytes in the skin – if due to changes in timing they are late to arrive to some distal parts, e.g., paws and tail-tips, those part will be white. Neural crest cells also migrate to become the adrenal medulla – that little part of the body that releases (nor)epinephrine (adrenaline). If fewer of those cells arrive there on time, less the animal will show stress-response later in life.

There appears to be tight correlation between timers that act on different scales, e.g., developmental and circadian timing, circadian and fast behavioral timing, circadian and seasonal timing, etc.

I always wished I could get a lab, some foxes, an IACUC approval and some money to run these animals through a battery of standard experiments comparing dogs, wild foxes and domesticated foxes on all sorts of parameters of circadian rhythms, photoperiodism (they did change their seasonality patterns of breeding, after all), etc.

The bottom line is that a subtle change in timing of expression of a single developmental gene, something one can select for by choosing one of the traits (in this case a behavioral trait), will affect the change in timing of expression in many other genes. The difference between wild and domesticated foxes may not be in any DNA sequence at all – it could presumably be all epigenetic (see also). Sequence differences would arise later, as the two populations are not inter-mixing any more (for over 60 years now).

When you put together development, genetics and evolution, you can see that big changes (or, really, any changes at the very beginning of the evolutionary change) in DNA sequence are not necessary for big changes in entire suites of phenotypic traits. But in the 1950s, the bean-bag deterministic genetics was the norm, so the Belyaev experiment was a big jolt to the scientific community in the West (not so much for the Russian evolutionary biologists, though), so we need to look at this experiment through a decent grasp of history.

Now, I’d like to know what is the state of the experiment today. Ten years ago, the project appeared doomed – they had to sell foxes for fur in order to keep going at a small scale. Has this been fixed? Has anyone from the West help finance the continuation of the project? Has anyone in the West acquired some of the foxes and continued with the project? What are the recent developments?

Related at Scientific American:

Man’s new best friend? A forgotten Russian experiment in fox domestication by Jason G. Goldman

Learning from Domesticated Foxes by The Dog Zombie

The Russian Fox Study by Jason G. Goldman

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 cellular 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 synchronicity 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 bringing the food home. When that happens, the behavioral development of other workers speeds up dramatically – in almost 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 rhythmicity 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 [April 2009], 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: the numerous clocks in our bodies are not synchronized with each other. We have evolved to be diurnal animals, entrained to environmental light cycles and not traveling over many time zones within hours, or working around the clock. Social insects have evolved a different strategy to deal with the potentially ill effects of shift-work: switch off the clock entirely until one develops far enough that time-keeping becomes a requirement.

References:

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) DOI: 10.1186/1472-6785-9-7

Editors (including Jason here at the network) at ScienceSeeker.org and editors (including Krystal here at the network) at ResearchBlogging.org filter the best science blog posts each week.

Ed Yong’s weekly linkfests (like this one) and monthly Top 10 choices he’d pay for (see this for an example) are must-bookmark resources.

Some other bloggers are occasional or regular sources of links I pay attention to, e.g., John Dupuis on academia, publishing, libraries and books, Chad Orzel on academia and science – especially physics, Mike the Mad Biologist on science and politics, and the crew at the Knight Science Journalism Tracker for the media coverage of science. And at the NASW site, Tabitha Powledge has a must-read On science blogs this week summary every Friday.

Most of the articles and blog posts I read every day are brought to my attention by my friends on Twitter, Google Plus and Facebook, I get some through email notifications, as well as gleaned from ScienceBlogging.org and ScienceSeeker.org science blog aggregators. I then share a LOT of those links to my followers on Twitter, Facebook and Google Plus every day.

Every workday around midnight I post a linkfest on The Network Central to make it easier to see our network posts if you missed them during the day. Khalil and I take turns highlighting the best work by up-and-coming science writers on The SA Incubator blog. Weekly posting of the ever-growing list of posts submitted for the Open Laboratory is another resource. SciAm homepage is also set as a collection of filters – we decide what goes into “Blogs” box, what in the “Latest News” feed, what in the “Science Agenda” on top of the page, and what to collect into “In-Depth Reports” over time.

Now I will also start a weekly collection of links that are “best of the best” of everything I read over a period of a week – not the posts from #SciAmBlogs, but the rest of the Web: other blogs and other media sites. That means a lot of cutting! I mean, I tweet TONS of links every day! Choosing the best will not come easy to me, so this is a good exercise for me as well, and I hope will become a useful resource to you.

I’ll try to do this every Friday, time of day dependent on travel, work, life etc. Let me know in the comments if you have suggestions for formatting, timing, etc.

Blog of the Week:

Academic Panhandling: The art of granting for your supper. Everything you ever needed to know about writing grant proposals, written by a professional grant writer.

Top 10:

The Moscow Rules – Science Edition: Part 1, Part 2, Part 3, Part 4, Part 5, Part 6, Part 7, Part 8, Part 9 and Part 10 by Zen Faulkes, guest-blogging at Scientopia:

The Moscow Rules were directives that undercover American intelligence agents allegedly used in the Cold War. The rules were there to increase agent’s chances of making it out safely.

Sometimes, being in academic science can feel like being enemy territory in a cold war. You are often in strange territory (new lab), with many unfamiliar people (other grad students, post-docs, faculty) whose motivations are unclear. You might not trust them completely (especially administrators). There might not be the risk of attempted assassination by having poison injected into you with a specially built umbrella, but there’s enough similarity that the Moscow Rules can still apply…

If You Want A Lizard To Run Fast, Yell At It by Jonathan Losos:

…“As you well know, some days things just don’t seem to go well when testing whole animal performance. On one of those days out of frustration, fatigue, etc., we simply yelled at an apparent “slacker” lizard in jest. Much to our surprise this seemed to make a difference. We were also aware of the two recent papers for other species of lizards in which sound appeared relevant to behaviors associated with detecting threats. So, we figured what the heck, why not test for such effects systematically. Unlike many of the studies that you and others have performed with anoles, unless we simply can’t get a lizards to run along the racetrack or they appear unhealthy, we include data from all of the individuals rather than subjectively rating the trials for their quantity. Perhaps, some of the gains in speed associated with our yelling were greatest for those individuals that otherwise might have been discarded after receiving a poor subjective quality rating. Of course, we lack a simple way of determining this. Similarly, we have not yet methodically tested for whether expletives are more effective that milder language.”…

Invisible aliens: they’re not life as we know it — yet by John Rennie:

Both publications posit that life, at its most abstract, involves a thermodynamic disequilibrium. That is, life involves physical structures that can only maintain their integrity with inputs of energy. These physical structures will require covalent bonds between atoms (to allow nontrivial chemical reactions), so the environment in which life appears must allow such chemistry to occur. Some kind of liquid, but not necessarily water, would therefore also be necessary to enable those reactions. Finally, some molecules in the living system would need to be capable of Darwinian evolution for the life to arise. (Take note, creationist doubters of evolution: it is now a useful part of the definition of life!)

From theory and experiments, both papers argue that life with these traits could evolve under a wide (but definitely limited) range of environments. Carbon-based life on worlds with liquid water might represent a particularly versatile and common set of solutions, but biochemistry could go in many directions even on Earthlike worlds. And on planets and moons where terrestrial life would perish instantly, life based on silicon instead of carbon or liquid hydrocarbons instead of water might thrive…

Plastic Lessons by Shara Yurkiewicz:

I always feel awkward when I talk to plastic patients. The simulation mannequins are impressive: their eyes blink, their chests expand as they breathe, they have pulses, they bleed, they burn. A screen monitors vital signs: I administer a pressor and a dipping blood pressure perks up, or I order a beta blocker and a racing heart rate slows. A physician in the next room lends her voice to play the patient, responding to what I do and say. A physician in the same room becomes a tech, relying results of my tests and nudging me through the next steps when I veer off course….

Twilight of the giants in taxonomy by Emmett Duffy:

In an important sense, nothing exists until it’s given a name. And in the living world of organisms, names—official, scientific names—are assigned by unique creatures called taxonomists, experts in the minutiae of structure and biology of particular groups of organisms, working according to a strict and arcane body of rules of biological nomenclature. These individuals tend to be specialists—sages of whales, anglerfishes, microscopic worms that live only between the grains of sand on beaches, microscopic algae, purple sulfur bacteria, and everything in between…

Is Technology Destroying Your Relationships? by A.V.Flox:

Social networks put a number on those weak ties, but we all have weak ties in our meatspace lives. Marche bemoans how we use machines to check out at the grocery store instead of waiting in line with other people to have our purchases rung up by an actual human. But I wonder — even if you were to speak to the woman giving you dirty looks because you were buying a product with a big carbon footprint, can you actually call that a meaningful relationship?

I talk to people all the time — cab drivers, waiters, flight attendants, the guy at the post office, my manicurist, my barista, the boys at the convenience store where I buy my cigarettes, the guy at the newsstand. I am there, in the flesh. Does this mean our connections are any more meaningful than a like or a plus on social media?

Weak ties exist. They’re everywhere. All we have to do to make them meaningful is take the chance to go deeper. This is as true online as it is offline.

What does it mean to say that something causes 16% of cancers? by Ed Yong:

…executives and policy-makers love PAFs, and they especially love comparing them across different risk factors. They are nice, solid numbers that make for strong bullet points and eye-grabbing Powerpoint slides. They have a nasty habit of becoming influential well beyond their actual scientific value. I have seen them used as the arbitrators of decisions, lined up on a single graphic that supposedly illustrates the magnitude of different problems. But of course, they do no such thing…

The Mysterious Case of the Vanishing Genius by Mike Martin:

Margie Profet was always a study in sharp contradictions. A maverick thinker remembered for her innocent demeanor, she was a woman who paired running shorts with heavy sweaters year-round, and had a professional pedigree as eccentric as her clothing choices: Profet had multiple academic degrees but no true perch in academe. In the late 1980s and early 1990s, Profet published original theories about female reproduction that pushed the boundaries of evolutionary biology, forcing an entire field to take note. Indeed, back then it was hard not to notice Margie Profet, a vibrant young woman who made a “forever impression” on grade school chums and Harvard Ph.D.s alike. Today, the most salient fact about Profet is her absence. Neither friends, former advisers, publishers, nor ex-lovers has any idea what happened to her or where she is today. Sometime between 2002 and 2005, Profet, who was then in her mid-40s, vanished without a trace…

Fear fans flames for chemical makers by Patricia Callahan and Sam Roe (see also Part 2 Big Tobacco wins fire marshals as allies in flame retardant push and Part 3 Distorting science):

Manufacturers of fire retardants rely on questionable testimony, front groups to push standards that boost demand for their toxic — and ineffective — products

Asymmetrical snakes by Andrew Durso:

Animals have a long tradition of being bilaterally symmetrical – that is, of the left side and the right being nearly identical. Sure, there are a few exceptions – the human heart is nearly always farther to the left side, for instance. Snakes and other elongate, limbless animals sometimes stagger their paired organs (gonads, kidneys) so that one is in front of the other, to better fit in their cylindrical bodies. Most snakes have even done away with one of their two lungs. But the basic external body plan, the bones and muscles on the left and the right, are always mirror-images of one another, right?

Enter the pareatid snakes…

Science:

Drop the base to make bagels more delectable by Raychelle Burks:

Sometimes, just hearing that certain chemicals are in food just puts people off. “I think that a lot of people would be really surprised about the precise chemicals that are used to make their favorite foods,” said Dr. Hartings. Take Cool Whip for example. One of its ingredients is polysorbate-60, a chemical that helps give Cool Whip its puffy appearance. Polysorbate-60 moonlights as an ingredient in sexual lubricants like K-Y YOURS+MINE. Our foods contain all kinds of chemicals that have more than one job. Thankfully, one of those jobs is making food delicious.

Insects that skate on the ocean benefit from plastic junk by Ed Yong:

Imagine a world of two dimensions, a world with no up or down… just across. No climbing, falling, jumping, or ducking… just shimmying and sidling. Welcome to the world of the sea skater.

Sea skaters, or ocean striders, are small bugs. They’re relatives of the pond skaters or water striders that zip spread-eagled across the surface of ponds and lakes. Except they skate over the open ocean, eating plankton at the surface…

Problems in the neurozone by Pete Etchells:

Having a scan of your brain is a uniquely odd experience. I had one done once. I was loaded, torpedo-like, into a claustrophobia-inducing, cocoon-like chamber for nearly an hour, the first few terrifying minutes of which I spent desperately trying to recall whether I had actually passed that metal ball-bearing I swallowed when I was a kid. The machines themselves are pretty damn loud, but something about repetitive clunking noises seems to lull me into a state of relaxation, so I spent the majority of my time in the launch chamber trying not to snooze. Honestly, it was all quite enjoyable…

Abandoment issues by Dr. Al Dove, guest-blogging at NeuroDojo:

There exists on my hard drive a folder into which I loathe copying files, but only slightly less than I would loathe deleting them all together. It is a folder called “Aborted Manuscripts” and it is this folder which is the source of my shame. It is a graveyard of stupid ideas and of great ones poorly executed, of unfinished cogitations, of journal rejections, of unresponsive colleagues and of frustrating students. It’s a roadmap documenting 15 years of science (read: “me”) not doing what science (read: “me”) is supposed to do – get published…

Put Away The Bell Curve: Most Of Us Aren’t ‘Average’ by Shankar Vedantam:

The bell curve powerfully shapes how we think of human performance: If lots of students or employees happen to show up as extreme outliers — they’re either very good or very bad — we assume they must represent a skewed sample, because only a few people in a truly random sample are supposed to be outliers.

New research suggests, however, that rather than describe how humans perform, the bell curve may actually be constraining how people perform. Minus such constraints, a new paper argues, lots of people are actually outliers.

Human performance, by this account, does not often fit the bell curve or what scientists call a normal distribution. Rather, it is more likely to fit what scientists call a power distribution…

The real CSI: what happens at a crime scene? by Craig Taylor:

From the diver who finds the body parts, to the forensic specialist who identifies flecks of paint on the victim and the handwriting expert who examines the killer’s notes… What happens behind the yellow tape of one crime scene

Of mice and Marmaduke (and dinosaur farts) by Mike Argento:

EDITOR’S NOTE: The following column contains sophomoric humor and references to the bodily functions of dinosaurs and the size of certain anatomical features of mice, all in the name of science. If this kind of thing offends you, please skip this and go right to Marmaduke. That dog, he cracks us up…

Spacesuit In A Cave by Sarah Everts:

Most visitors to the million-year-old Dachstein Giant Ice Cave prefer to wear standard winter coats during visits to its freezing, icy interior. But for five days the Dachstein cave systems were a temporary lab for a squad of space scientists. Some 50 scientists assembled from three continents to use the UNESCO World Heritage site as a proxy for Mars—a first for the cave system, which normally hosts jazz concerts, modern art exhibits, laser shows, and a steady stream of tourists….

Experimental Biology Blogging: Self-promotion and ‘self-promotion’ by Scicurious:

But of course, this is because academics have two different kinds of self-promotion. One is ok, and one is not. One takes place in the ivory tower, and one involves the dreaded public…

1859′s “Great Auroral Storm”—the week the Sun touched the earth by Matthew Lasar:

Noon approached on September 1, 1859, and British astronomer Richard Christopher Carrington was busy with his favorite pastime: tracking sunspots, those huge regions of the star darkened by shifts in its magnetic field. He projected the Sun’s image from his viewing device onto a plate of glass stained a “pale straw colour,” which gave him a picture of the fiery globe one inch shy of a foot in diameter…

The Physics of Spilled Coffee by Jon Cartwright:

…Krechetnikov and his graduate student Hans Mayer decided to investigate coffee spilling at a fluid dynamics conference last year when they watched overburdened participants trying to carry their drinks to and fro. They quickly realized that the physics wasn’t simple. Aside from the mechanics of human walking, which depends on a person’s age, health, and gender, there is the highly involved science of liquid sloshing, which depends on a complex interplay of accelerations, torques, and forces. …

Why Do Conference Talks Suck, and How Can We Change That? by Matthew R. Francis:

…Yes, some speakers are better than others, and a few of the 42 talks I heard were very good. Also, I know I used to commit many of the same sins I witnessed in talks yesterday and the day before, so as I list the problems, I’ll flag my own bad habits (current and former). Based on conversations with my friends, this is not a problem limited to particle physics conferences, much less to physics conferences in general: it’s endemic in science, and perhaps most academic fields…

Sleek, Smart Spacesuits Are on the Horizon by Amy Shira Teitel:

Spacesuits are poised to go the way of the cell phone – once bulky and cumbersome, researchers are working on making them slim and smart. In the future, astronauts might be wearing specially engineered garments that combine the life-preserving features of a spacesuit with augmented reality technology that could intuit the wearer’s needs…

How and Why Neuroscience should be taught in School by TheCellularScale:

…Neuroscience is sort of where genetics was 20-30 years ago: The scientific frontier, fascinating to the public, changing the general worldview, raising ethical questions, science fiction’s closest reflection in reality. This has its benefits and its downfalls. There is currently strong general enthusiasm for neuroscience for just these reasons, but because everything ‘neuro’ is so exciting, the risk of media misrepresentation is high and the misuse of neuroscience concepts and terms by pseudo-science is common. …

Fetal Attraction by Robert Krulwich:

…Dr. Johnson says cells from fetal boys and girls have been found in mothers “four to five decades following the last pregnancy.” That fetus may have grown into a middle aged pharmacist, and still his cells are inside his mother. Cells wouldn’t persist in foreign body for NO reason. They must be doing something, but what?…

On Biocultural Anthropology by Daniel Lende:

…what brings many students into anthropology, and still impassions me about the field, is that it does approach the question of “What does it mean to be human?” in the broadest, most interdisciplinary way. And it strikes me that we have some core analytical approaches to that question that matter, and that this style of thinking is what really makes up the holism of anthropology, rather than a particular commitment to four-fields and working across the different sub-disciplines. This human lens includes a comparative approach, an attention to variation across time and space, a recognition that we as researchers inevitably bias our own data, and, yes, a commitment to drawing on multiple strands of research…

94 Elements by The 94 Elements team:

There are 94 naturally occurring elements, from Hydrogen to Plutonium, and together they make up everything in the world. The stories of the elements are the stories of our own lives, revealing the details of our personal lives, the patterns of our economies, and our relationships with our natural resources.

94 Elements is a new global filmmaking project, exploring our lives through the lens of the elements. The project is producing a collection of stories by different filmmakers about the endless ways the elements touch our daily lives. Each filmmaker takes one element as the basis for a film around how it’s used. The films are surprising and moving human stories – this is not about science, but about our human relationships with our mineral resources.

How Does the FDA Monitor Your Medical Implants? It Doesn’t, Really by Lena Groeger:

Each prescription drug you take has a unique code that the government can use to track problems. But artificial hips and pacemakers? They are implanted without identification, along with many other medical devices. In fact, the FDA doesn’t know how many devices are implanted into patients each year – it simply doesn’t track that data.

The past decade has seen numerous high profile cases of malfunctioning medical devices, which have led to injury or even death. Critics say the FDA’s minimal monitoring of devices contributes to these problems….

Leptin: Linking Malnutrition and Vulnerability to Infection by Michelle Ziegler:

As long as leptin levels stay within normal levels, all of the functions displayed above function normally. As the leptin levels drop, many of these functions are adversely effected. It is a wide-spread trigger for a starvation response. Why cripple the immune response during starvation? My best guess would be because of the huge energy expenditure required to keep the immune response running normally, especially in cellular proliferation.

Experts debate what makes a healthy vagina by Anna Salleh:

New US findings suggest our accepted definition of a healthy vagina could be ethnically biased, say some researchers, but others caution against over-interpreting the data.

A new study published today in Science Translational Medicine found, what an accompanying commentary describes as, an “unexpected and astonishing” variability over time in the vaginal bacterial communities of apparently healthy women….

The Ph.D. Now Comes With Food Stamps by Stacey Patton:

…A record number of people are depending on federally financed food assistance. Food-stamp use increased from an average monthly caseload of 17 million in 2000 to 44 million people in 2011, according to the U.S. Department of Agriculture’s Web site. Last year, one in six people—almost 50 million Americans, or 15 percent of the population—received food stamps.

Ms. Bruninga-Matteau is part of an often overlooked, and growing, subgroup of Ph.D. recipients, adjunct professors, and other Americans with advanced degrees who have had to apply for food stamps or some other form of government aid since late 2007….

Nicholas Kristof and the Bad, Bad Chemical World by Deborah Blum:

…Because his secondary crusade of the last few years, you know, the one against evil industrial chemicals, is really starting to annoy me. This is not saying that he’s entirely wrong – there are evil industrial chemicals out there. And, in many cases, they aren’t as well researched or as well regulated as they should be.

But if we, as journalists, are going to demand meticulous standards for the study and oversight of chemical compounds then we should try to be meticulous ourselves in making the case. And much as I would like it to be otherwise, I don’t see enough of that in Kristof’s chemical columns. They tend instead to be sloppy in their use of language, less than thorough, and chemophobic enough to undermine his legitimate points….

How Academic Biologists and Physicists View Science Outreach by Elaine Howard Ecklund, Sarah A. James and Anne E. Lincoln:

Scholars and pundits alike argue that U.S. scientists could do more to reach out to the general public. Yet, to date, there have been few systematic studies that examine how scientists understand the barriers that impede such outreach. Through analysis of 97 semi-structured interviews with academic biologists and physicists at top research universities in the United States, we classify the type and target audiences of scientists’ outreach activities. Finally, we explore the narratives academic scientists have about outreach and its reception in the academy, in particular what they perceive as impediments to these activities. We find that scientists’ outreach activities are stratified by gender and that university and disciplinary rewards as well as scientists’ perceptions of their own skills have an impact on science outreach. Research contributions and recommendations for university policy follow.

Blue-eyed-people-are-all-related zombie news by Jon Wilkins:

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

Conceptual Replication by Dave Nussbaum:

There is no substitute for direct replication – if you cannot reproduce the same result using the same methods then you cannot have a cumulative science. But conceptual replication also has a very important role to play in psychological science. What is conceptual replication? It’s when instead of replicating the exact same experiment in exactly the same way, we test the experiment’s underlying hypothesis using different methods…

Replicating Dissonance by Dave Nussbaum:

Another reason conceptual replication is so important is that if the field relies exclusively on direct replication then they risk replicating the same mistakes as well. Today I wanted to illustrate this risk by looking back at the history of one of social psychology’s most influential theories: cognitive dissonance. The richness and depth of Cognitive Dissonance Theory is a result of dozens of conceptual replications. I suggest that, had it not been for conceptual replication – had dissonance only been tested and re-tested in the original paradigm (Brehm’s Free Choice Paradigm) – the theory may not have stood up to recent criticisms directed at that particular paradigm…

Chimp acts like jerk, gets praised by scientists by Eoin O’Carroll:

A chimpanzee at Furuvik Zoo in Sweden has been lauded for his ‘innovation’ and ‘sophisticated cognitive skills,’ after behaving like a complete schmuck.

What is Peru’s dolphin and pelican die-off telling us? by Al Dove:

As many as 900 dolphins and over 4,000 pelicans have washed up dead on the beaches of northern Peru in the last couple of months, (see news coverage here, here and here), leading to a flurry of activity as various authorities and other interested parties move to find out what is going on. Experts cited in the news coverage suggest that unusually warm surface waters (10F higher than the season average) are changing the swimming patterns of the huge anchovetta schools off the coast of Peru, driving them deeper and out of the diving range of pelicans. In other words, the pelicans appear to be starving. The dolphins on the other hand, have shown a high prevalence of infection with morbilivirus, which is an infectious disease…

Why a Sperm Cell Is Like a Roomba by Elizabeth Preston:

A sperm cell, much like an expensive robotic vacuum cleaner, is a minimally intelligent body on a mission. Both the Roomba and the male gamete have to navigate a walled space without much idea where they’re going or why. And although it won’t clean your floors on the way, the sperm cell uses some of the same strategy as the robot vacuum…

In the Spring, Bat Moms Choose Girls by Elizabeth Preston:

Naturally a mother bat is happy to welcome into the world a bouncing baby whatever, as long as it has all its fingers and toe-claws. But she also wants her little one to have every advantage she can give it. So when spring comes early, big brown bats prefer to keep their female embryos. Unwanted males are reabsorbed into their mothers’ bodies as if they never existed…

Media, Publishing and Technology:

Science and Truth: We’re All in It Together by Jack Hitt:

…By now, readers understand that the definitive “copy” of any article is no longer the one on paper but the online copy, precisely because it’s the version that’s been read and mauled and annotated by readers. (If a book isn’t read until it’s written in — as I was always told — then maybe an article is not published until it’s been commented upon.) Writers know this already. The print edition of any article is little more than a trophy version, the equivalent of a diploma or certificate of merit — suitable for framing, not much else.

We call the fallout to any article the “comments,” but since they are often filled with solid arguments, smart corrections and new facts, the thing needs a nobler name. Maybe “gloss.” In the Middle Ages, students often wrote notes in the margins of well-regarded manuscripts. These glosses, along with other forms of marginalia, took on a life of their own, becoming their own form of knowledge, as important as, say, midrash is to Jewish scriptures. The best glosses were compiled into, of course, glossaries and later published — serving as some of the very first dictionaries in Europe.

Any article, journalistic or scientific, that sparks a debate typically winds up looking more like a good manuscript 700 years ago than a magazine piece only 10 years ago. The truth is that every decent article now aspires to become the wiki of its own headline. …

Neuroscience: Bloggers rule? by Paul Raeburn:

..We might be hard put to find any area of science coverage that hasn’t been subject to those kinds of distortions. Coverage of Lipitor and its ilk was certainly as likely to contain dramatic headlines, and particular agendas, including those of pharmaceutical companies. And ideological arguments? It depends upon what the meaning of “ideological” is…

Brain waves by Curtis Brainard:

From advice about “exercising your mind” to treatises on “the gay brain,” media coverage of neuroscience in the UK often pushes “thinly disguised ideological arguments” and reinforces artificial divisions between social groups, according to a new study….

What Will Become of the Paper Book? by Michael Agresta:

…In the past several years, we’ve all heard readers mourn the passing of the printed word. The elegy is familiar: I crave the smell of a well-worn book, the weight of it in my hands; all of my favorite books I discovered through loans from a friend, that minor but still-significant ritual of trust; I need to see it on my shelf after I’ve read it (and I don’t mind if others see it too); and what is a classic if not a book where I’m forced to rediscover my own embarrassing college-age marginalia?

Luddites can take comfort in the persistence of vinyl records, postcards, and photographic film. The paper book will likewise survive, but its place in the culture will change significantly. As it loses its traditional value as an efficient vessel for text, the paper book’s other qualities—from its role in literary history to its inimitable design possibilities to its potential for physical beauty—will take on more importance. The future is yet to be written, but a few possibilities for the fate of the paper book are already on display on bookshelves near you…

Abraham Lincoln Did Not Invent Facebook: How a Guy and His Blog Fooled the Whole Wide Internet by Megan Garber:

…He expected — and banked on — the web’s virality, he says; he didn’t anticipate, though, how eagerly that web’s self-defined news sources would pass along his “discovery.” And he assumed people would figure out the story’s hoaxiness much more quickly than they actually did — and, then, that the corrective powers of the social web would make that joke clear within the first hour or so after the story went live…

WWW inventor warns against call for comment sections to be placed under Data Rentention Act by Kristine Lowe:

…Berners-Lee said he was concerned about how increased demands for monitoring the web, both from governments looking for greater powers to track down terrorists and companies looking to trade our personal web data for commercial purposes, threatens the very infrastructure of the web.

He described his worry that people in the end will no longer trust and use the web for e.g. researching sensitive things like depression if they fear everything they do online is being monitored…

7 New Educational Startups Founded By Minorities in Tech by Wayne Sutton:

One of today’s most challenging yet promising markets is the educational system. If you want to see startups hungry to disrupt an industry, look no further. Founders are trying to solve the problems plaguing our education system: including reconciling student debt, providing students with the skills required to land a job both before and after graduation, and offering the best course material online regardless of age, location and educational level…

5 things med students can do to engage in social media and medicine by Josh Herigon:

One topic we neglected, however, was what current medical students can do right now to get their foot in the door and begin engaging in the social media and medicine conversation. I had hoped to get to this topic during my panel discussion, but there just weren’t enough hours to cover everything. Below is my attempt to remedy this omission. Here are a few simple things you can do:

Blinding us with science journals by Peter McKnight:

A competitive university culture that discourages the sharing of knowledge has led to the publication of many flawed and fraudulent studies…

The Arrogance of Publishers vs. Academic Culture – Why the Outcome Is Virtually Certain a scholarly kitchen metaphor by Mark Carrigan:

Imagine a situation where homes had no kitchens and utensils were unavailable. We would all be dependent on cafes and restaurants to eat and, it follows, our idea of what it is to prepare food would be exhausted by those working in such a capacity within these establishments. Now introduce kitchens into homes and affordable utensils into shops. Suddenly we can cook meals at home. Obviously the quality of the infrastructure is lower and there’s less expertise. For the sake of the thought-experiment, assume kitchens and utensils appeared suddenly, to an extent profoundly disruptive of established practices of going out for every meal. The meals cooked at home would be of poor quality, probably pragmatically orientated and often imitating (poorly) the meals available in restaurants and cafes.

The Science of Obituaries: Dead Pools, Obits in the Can and More by Arthur S. Brisbane:

Mr. McDonald said The Times currently has 1,500 advance obits in the can – “and we’re adding about 250 a year. Even if you subtract the number of those we’ll publish in a given year – say, 50 – the archive is growing significantly.”…

The Psychological Prerequisites of Punditry by Julian Sanchez (also see response by Andrew Sullivan):

….The nice way to say this is that selects for pundits who have a thick skin—or forces them to quickly develop one. The less nice way to say it is that it forces you to stop giving a shit what other people think. Maybe not universally——you’ll pick out a domain of people whose criticisms are allowed to slip through the armor—but by default….

Four perspectives on communicating your research, and then one more. #EB2012 by William Gunn:

…The most popular sentence of the whole session was “Don’t underestimate your audience’s intelligence, but do underestimate their vocabulary.” In other words, drop the jargon if you want the public to get what you’re saying. …

Filter-then-publish vs. publish-then-filter by Mike Taylor:

…In the face of such a flood of information, no-one can read everything that’s made it through the filters into all their favourite journals. So in practice what actually happens is that each of us filters again – finding relevant publications in a huge range of journals by the social web we’re in: mailing lists, blogs, Twitter, and so on. I believe some people even use FaceBook….

10 Commandments of Twitter for Academics by Katrina Gulliver:

…Twitter is what you make of it, and its flexibility is one of its greatest strengths. I’m going to explain why I have found it useful, professionally and personally, and lay out some guidelines for academics who don’t know where to start….

Fungible by Stijn Debrouwere:

A treatise on fungibility, or, a framework for understanding the mess the news industry is in and the opportunities that lie ahead.

Why Publishers Don’t Like Apps by Jason Pontin:

…But the real problem with apps was more profound. When people read news and features on electronic media, they expect stories to possess the linky-ness of the Web, but stories in apps didn’t really link. The apps were, in the jargon of information technology, “walled gardens,” and although sometimes beautiful, they were small, stifling gardens. For readers, none of that beauty overcame the weirdness and frustration of reading digital media closed off from other digital media. …

The brilliant Joe Weisenthal by Felix Salmon:

Appelbaum is absolutely right that Weisenthal stands apart by starting earlier, writing more, publishing faster. That’s who Joe is. But he’s absolutely wrong that there’s an “intensely competitive world of financial blogging, dominated by young men who work long hours and comment on every new development”. Go on — name a single other financial blogger who fits that description. I’m waiting. There’s the anonymous group blog ZeroHedge, perhaps. But the fact is that Henry Blodget, in hiring and promoting Joe, has succeeded in identifying and harnessing and leveraging a nervous energy which has been there all along. He didn’t start with some kind of inhuman job description and then hire Joe to fill it; he found Joe and then basked in the fruits of encouraging him to simply be his natural self.

River of News — FTW! by Dave Winer:

…I don’t think that fancy layout trumps newness. The name “news” tells you what’s important about news. Newness. So if you follow that clue, it leads you to the obvious conclusion that news should present first the newest bits we have. What’s next? The second newest bits. And third, fourth and so on. permalink
News is one of those things that is that simple. But it takes people a while to get there if they don’t allocate the time to take walks in the park and think about this stuff in an organized way….

Blogging and Kickstarter go together by Dave Winer:

…But once the users can communicate with each other, we will be able to pool our experience, and given enough time, smart users will learn the technology well enough to make the products that (key point here) they know there is demand for. Because they are the ones demanding it….

The Pernicious Myth That Slideshows Drive ‘Traffic’ by Alexis Madrigal:

…If you’re trying to juice page views, your staff will ineluctably be forced to make galleries. Where else can they get a 10x or 20x multiplier on their work? I can guarantee you that will not help you break the kinds of stories or do the kinds of analysis that will keep people coming back. Not only that, but it’s demoralizing to your best people, the ones who want to be out there producing their best work.

Worse, readers may click through your slideshow, but they’ll hate you a liiitttle bit more than they did when they got to the site. And I bet they’ll feel the same way about whatever advertiser was unlucky enough to get stuck on the page with some stupid thing that a reporter did with a little bit of hate in his heart and fingertips. ….

Today my guest is Sarah Chow (blog, Twitter).

Welcome to A Blog Around The Clock. Would you please tell my readers a little bit more about yourself?

Currently, I am a PhD student at the University of British Columbia studying Pacemaker proteins. These are proteins that help make your heart beat. The main goal is to understand how these proteins are regulated by a molecule called cAMP, by measuring the thermodynamic properties of the reaction between cAMP and the Pacemaker protein.

Although my current research focuses on very small microscopic things, my undergraduate degree is in Kinesiology, which focuses on macroscopic portions of the body. I also have a certificate in health and fitness studies.

Understanding how the body functions macroscopically and connecting it microscopically is what brought me do my PhD research today.

Tell us a little more about your career trajectory so far?

Out of high school, I wanted to be a Physical Education teacher as well as a track and field coach, because I had such great mentors in those fields. After doing a work study semester at the local science centre teaching children, it didn’t feel like the right fit for me.

I fell into research serendipitously. I casually mentioned to my anatomy teaching assistant I was interested in doing scientific research. She immediately introduced me to a professor within the department of kinesiology. Seven years later, that professor, is now, and still, my supervisor.

How did you first start becoming interested in Science Communication?

I have always been interested in communicating science, in fact, before switching from my masters degree to a PhD, I seriously considered applying to a Masters in Journalism Program. But, my research project was doing so well at the time, I decided to stick with it.

In August 2011, I attended the Banff Science Communication Program in Banff, Alberta, Canada and it changed my life. My classmates were a mixture of graduate students, science writers, science filmmakers, and science journalists. The faculty was comprised of veterans in their fields: two television directors from the Discovery Channel, four science communicators who have written books, worked as editors for Scientific American, created podcasts, blogs, and even hosted their own science television show. I ate, slept and breathed science communication for two-weeks. And within this short period of time, I created a podcast, a short science film, wrote a science article for the general public, and a website.

At the end of those two weeks, I was a science communicator convert. My heart told me, Sarah, this is who you are.

Why is science communication important to you?

I believe we have the power to govern our own path in life by making informed choices. Understanding how science is the basis of everything that surrounds us can help that process. The reason why I do research is not only to understand how the heart works, but in the bigger scheme of things, we all have this pacemaker protein in common. If that protein fails, not only is your life affected, but your surrounding loved ones lives, your community and your world is now changed because of this one little protein dictating the rhythm of your heart. Having people understand how and why science is so important and the global impact it can have on ones life is why I believe science communication is important.

What is taking up the most of your time and passion these days? What are your goals?

My main goal is to finish my PhD degree by finishing up experiments and writing my thesis.

However, a lot of my time right now is dedicated to improving my science communication skills. I’ve been blogging regularly on my website, which is a mixture of podcasts, video, and writing. My website is more of an “online laboratory” where I can experiment with different styles of communication. I also podcast for Experimental Podcast, am editor for Science Seeker News, TV show co-host for UBCevents on campus and taking improv and acting lessons to improve my presentation skills.

I am also one of the co-organizer of ScienceOnlineVancouver, a monthly discussion series focusing on issues and topics surrounding science communication.

What aspect of science communication and/or particular use of the Web in science interests you the most?

I am most interested in communication science via “transmedia”, using podcasting, video blogging and combining photos with audio clips to tell an engaging science story to the public. I really like to immerse my readers into my stories by engaging their sense by using sounds and visuals.

The web is useful because I can use sound, photos, words, movies, to create a three-dimensional story, which can be difficult via more traditional forms of science communication such as print.

How does (if it does) blogging figure in your work? How about social networks, e.g., Twitter, Google Plus and Facebook? Do you find all this online activity to be a net positive (or even a necessity) in what you do?

Blogging and tweeting about my work helps me to better understand my research and break it down into easier bits for me to digest and drill into my brain.

In general, blogging, twitter, google plus and facebook are all different avenues to give me a voice and showcase my interest. Now is my voice being heard? That’s a different question. But it allows me to interact and connect with people who are interested and passionate about science and science communication. It helps me broaden my community, which would not be possible without social media.

What was the best aspect of ScienceOnline2012 for you? Any suggestions for next year? Is there anything that happened at this Conference – a session, something someone said or did or wrote – that will change the way you think about science communication, or something that you will take with you to your job, blog-reading and blog-writing?

Being at Scio12 reminds me of the TV show series Cheers theme song:

Makin’ your way in the world today takes everything you’ve got.
Takin’ a break from all your worries, sure would help a lot.
Wouldn’t you like to get away?

Sometimes you want to go, where everybody knows your name,
and they’re always glad you came.
You wanna be where you can see, our troubles are all the same,
You wanna be where everybody knows your name.

It’s a safe, encouraging and inspiring place to be to share ideas. It’s a community.

The best advice I got from Scio12 was from @DrRubidium and @davidmanly’s session. Just hit the damn submit button and don’t look back. (That may be paraphrased a bit, but that’s how I remember it.)

What do you do in your spare time? If you have any.

I enjoy running, biking, hiking and volleyball. Basically anything that keeps me outdoors and active. I also like baking and reading a good book.

Thank you! Hope to see you again in January.

Looks great, inside and outside!

Also yesterday, we discovered that the book is now listed on Amazon.com so you can start pre-ordering it. Just click right over here!

Today my guest is Joe Kraus (blog, Twitter).

Welcome to A Blog Around The Clock. Would you, please, tell my readers a little bit more about yourself? Where are you coming from (both geographically and philosophically)? What is your background? Any scientific education?

I was born and raised in Southern Wisconsin in the late 1960s and 1970s. I went to Beloit College from 1985-1989 (with a short stint of engineering education in 1988) where I got my BS in Physics. Once I graduated college, my interests turned to astronomy for a time when I worked for a high end amateur telescope manufacturing company. My wife got her Masters in Statistics, and we ended up moving to Maryland just outside of Washington DC in 1991. There was a small recession going on, and I had a hard time finding a professional job with only a BS.

I always liked computers and libraries, and in the early 1990s I learned more about this new/old thing called the Internet. In 1993, I started the second phase of my life by attending graduate school at the University of Maryland, College Park in Library & Information Science. After I got my MLS in 1995, we moved to northern Virginia for a little while where I was the engineering librarian at George Mason University. By 1997, we were still feeling a little claustrophobic in the Washington DC metro area. We were able to move out to Denver, Colorado in early 1998, and I have been at the University of Denver as the Science & Engineering Librarian since then.

Tell us a little more about your career trajectory so far: interesting projects past and present?

I have been involved in the Special Libraries Association (SLA) since 1995. I was the Chair of the Physics-Astronomy-Mathematics Division in 2007, and I was the Chair of the Sci-Tech Division in 2011. As chair of those two divisions, I provided program planning for two different annual SLA Conferences. With the rise of the social web, I have gotten more involved with other organizations, such as the Library Society of the World (LSW. With the help of several other LSW participants, we organized a library Unconference in 2008. In 2009, I joined the editorial staff and helped launch the Open Access journal Collaborative Librarianship. I also post items to the Collaborative Librarianship News blog. In 2010, I helped organize another unconference, but this one was targeted to science and engineering librarians. We are organizing the 2nd STELLA Unconference later this year in New York City.

What is taking up the most of your time and passion these days? What are your goals?

As the Science & Engineering Librarian at DU, I help a lot of students and faculty learn about and use scientific databases and journals. I have also been writing and reading about scholarly communications issues. I have a passion for blogging and telling people about the wonderful world of science.

What aspect of science communication and/or particular use of the Web in science interests you the most?

The Internet is such an awesome way for people to share information and connect with one another. I am particularly interested in advocating for Open Access (and other cost-effective methods) to journal articles and Open Data proposals.

How does (if it does) blogging figure in your work? How about social networks, e.g., Twitter, Google Plus and Facebook? Do you find all this online activity to be a net positive (or even a necessity) in what you do?

I am on a lot of social networks, but the ones I find the most useful are Friendfeed, Twitter, and Diigo for tagging articles. My two main blogs are http://www.nuthingbut.net and http://www.sciencelibrary.org. Most of the social networks I use are marked at http://about.me/jokrausdu.

When and how did you first discover science blogs? What are some of your favorites? Have you discovered any cool science blogs by the participants at the Conference?

First off, I would like to thank Christina Pikas for introducing me to you and to many other science bloggers. Of the Science Online Librarian group, I highly recommend others follow Stephanie Willen Brown, John Dupuis, Bonnie Swoger, and Kiyomi Deards.

What was the best aspect of ScienceOnline2012 for you? Any suggestions for next year? Is there anything that happened at this Conference – a session, something someone said or did or wrote – that will change the way you think about science communication?

This is the best conference concerning the scientific communication industry. It has a great mix of people from science journalism, science publishers, science book authors, scientists, science bloggers, and science librarians. Concerning next year, I would like to see the topic of Open Access and Open Data addressed. We should have an update session concerning the “Declaration of Independence” from Elsevier.

I have two take-aways from the 2012 conference. 1) I enjoyed using the electrical outlets that were available in the middle of the seating sections. The person who duck taped all of the extension cords and 6 outlet power strips deserves a raise. This allowed people to live tweet and live blog the conference without fear of draining a battery. 2) I found the discussion of the conflict between science journalists (who paraphrase scientists for a lay audience) and the scientists (who write for narrow specialized audiences) to be productive. Both sides now have a better understanding of the views of the other.

Overall, I find this conference to be essential in my quest to better understand the scientific communication process. I am looking forward to coming back to North Carolina again in 2013. Many thanks go to Bora (and Anton and Karyn and many others) for putting together such a great conference.

Thank you! Hope to see you again in January.

Today my guest is Lali Derosier (blog, Twitter).

Welcome to A Blog Around The Clock. Would you, please, tell my readers a little bit more about yourself? Where are you coming from?

That’s never a short answer for me.  I was born in South America and educated in the States.  We moved around quite a bit.  Now that I am raising two American children, I am discovering odd gaps in my cultural education that I never realized were there. It does make for some occasionally hilarious family moments.  I came to the Orlando, FL area right out of college and I’ve been living and working here ever since.  It’s the longest amount of time I’ve stayed anywhere, so I guess this is where I am from.  At least, until the next time we move.  

What is your background? Any scientific education?

My focus on science began fairly early.  I went to the MAST Academy for high school (a maritime science magnet school), where I had a concentration in Oceanic and Atmospheric Sciences.  I went on to major in Biological Sciences at Smith College.  After teaching for about 10 years, I decided to pursue a Master’s in Science Education.  That experience was very eye-opening for me, in terms of how other educators teach and perceive science.  It was sobering.

Tell us a little more about your career trajectory so far: interesting projects past and present?

Thirteen years into teaching, I am only now beginning to feel like an expert in my field.  I used to think of myself as a “science teacher” but now I realize that I’m actually a “high school teacher.”  The fact that I teach science is almost incidental to how important it is to understand the developmental challenges of the adolescent age group.  Doing my Master’s program after teaching for a long time helped to crystalize some thoughts that I have had on changes that need to happen in teacher-training and curriculum development. The PhD bug has bitten me hard, but I am waiting a few months to see if the urge passes.

At my own school, I have been given the opportunity to develop a program for high school students to engage in authentic research in sciences.  I am open to anything from local science competitions to lab-based research internships to national science fairs.  It is pretty open ended, so the challenge for me has been to define the scope of the project so that it suits the needs of the students here.

It is easy to over-reach, and I’d rather start small and build it up over time.  I’m finding that I have to constantly curb my enthusiasm.  I am also excited to be working with Stacy Baker on her ScienceOnlineTeen event next year.  My focus for her unconference will be to address needs of teachers who are looking to use blogging as a learning tool, so that they can better support their students.

What is taking up the most of your time and passion these days? What are your goals?

Apart from the full time work and full time parenting, I’ve been thinking a lot about curriculum development.  Anti-science legislation makes it clear that science curriculum needs to be developed by teachers.  Specifically, by experienced teachers with science training.  I can’t imagine ever leaving the classroom, but I think if I did it would be to work with science education policy writing and curriculum development.  There is so much to learn in classroom teaching.  There will never be a time when I’ll feel I’ve mastered everything there is to learn.  That’s the fun of teaching.  Even if I give the same course for 50 years, each cohort has its own challenges and personality.  No two years are ever the same.

What aspect of science communication and/or particular use of the Web in science interests you the most?

The interactivity of the Web is incredibly appealing.  The internet has dramatically changed access to current research, scientists, and science writing.  The combination of journal publications, professional and personal blogs, and science journalism means that readers (students, in my case) can engage the research on multiple levels and in a combination of ways.  The immediacy with which scientific findings can be reported, dissected, commented on, and defended is wholly attributable to the internet.   

I get frustrated when I see educators trying to make the Web conform to traditional classroom styles of communication. Didactic, front-loaded teaching styles don’t mesh well with effective internet communication.  The internet is dynamic. That’s what makes it valuable. In order for teachers to be able to use Web 2.0 tools effectively, they’re going to need to loosen the reins quite a bit.  As technology becomes more accessible, more integrated into our daily lives, I am interested to see how educational practices will change.  The generational change of teachers will be very important too.  We’re in a transition right now, where some teachers consider themselves digital natives and others don’t.

How does (if it does) blogging figure in your work? How about social networks, e.g., Twitter, Google Plus and Facebook? Do you find all this online activity to be a net positive (or even a necessity) in what you do?

I am connected absolutely everywhere, and I wouldn’t have it any other way!  Blogging (as a writer) is new to me, but I use Twitter for microblogging, bookmarking, compiling to-be-read lists… you name it.  I don’t deny that some people take to connectivity better than others, but all of our students need to become proficient with it.  Schools can’t wait until they have to accept digital communication to get along.  They have to seek it out and innovate.  In many cases, our students know better than we do, and we should let them show us what works.

When and how did you first discover science blogs?

I stumbled on to the Deep Sea News crew early on in 2011.  Through them, I became aware of the main ScienceOnline event and my network just branched out from there.  I mainly use Twitter to keep up with blog posts from SciO12 attendees.  I find that I don’t read specific blogs so much as I sift through my twitter feed and click on titles that interest me.

Is there anything that happened at this Conference – a session, something someone said or did or wrote – that will change the way you think about science communication, or something that you will take with you to your job, blog-reading and blog-writing?

I’ll confess that I arrived at #Scio12 feeling like a bit of an impostor.  I was there on an information-gathering mission, hoping to bring back ideas that I could pitch to my administration for how we might integrate the Web into classrooms and curriculum.  As I have written elsewhere, what I found at #Scio12 was nothing short of inspirational.  I met people who, despite busy schedules and demanding work, find time to blog and engage online.

In my own work, I am always conscious of the fact that I have so much to learn.  I love asking questions and watching other teachers work.  I left with a “can-do” attitude and a lot of confidence in my own abilities to become a teacher for other teachers.  It isn’t such a large leap from how I already engage information online to doing my own writing and curating in a formal way.  This is what I most want to communicate to my fellow teachers.

Blogging for learning isn’t really an “add-on” to other things.  It is an extension of a skill that young people are developing naturally as they interact on the Web.  I also realised that people at every level of education, from grade school to post-professional, are encountering the same kinds of difficulties in how young people communicate.  I think blogs can be exploited to bridge the gap between informal and formal science writing.

Thank you!

New stuff:

What 3 Science Questions Do You Think the Presidential Candidates Need to Answer before November 6th?

Anthropologists love Scientific American

Events and updates:

A week in Edmonton

Sciencey events over the next few weeks

New ScienceOnline interviews:

ScienceOnline2012 – interview with Rebecca Guenard

ScienceOnline2012 – interview with Tanya Lewis

ScienceOnline2012 – interview with Kate Prengaman

ScienceOnline2012 – interview with Tracy Vence

And I republished a few posts from the old archives:

Flirting under Moonlight on a Hot Summer Night, or, The Secret Night-Life of Fruitflies

Some hypotheses about a possible connection between malaria and jet-lag

Whence Clocks?

Clock Evolution

Previously in the “Best of…” series:

2012

March
February
January

2011

December
November
October
September
August
July
June
May
April
March
February
January

2010

December
November
October
September
August
July
June
May
April
March
February
January

2009

December
November
October
September
August
July
June
May
April
March
February
January

Today my guest is Tracy Vence (LinkedIn, Twitter).

Welcome to A Blog Around The Clock. Would you, please, tell my readers a little bit more about yourself? Where are you coming from (both geographically and philosophically)? What is your background? Any scientific education?

Thanks for having me! It’s truly an honor. I am a scientist-turned-journalist in the sense that I studied biology as an undergraduate and journalism in graduate school. I’m now at GenomeWeb in New York, where I cover genomics research and related news for a monthly magazine called Genome Technology, and also curate life science-related stories of interest from around the Web for The Daily Scan and GenomeWeb Careers blogs.

I grew up a kid obsessed with science — entering robotics competitions after school, attending microbiology camp each summer, and taking apart just about everything I could get my hands on to figure out how it worked.

Naturally, I spent plenty of time in the lab as an undergrad, where I did independent research on aggressive behaviors in the water strider Aquarius remigis. I was fortunate to have linked up with two very supportive advisers, one of whom guided my A. remigis project (and gave me unrestricted access to all the gadgets, reagents, and Drosophila cultures in his lab), and the other who invited me to join his inaugural graduate-level science writing seminar. It was in that class I first learned about science writing: The Career. Before then I’d never considered the prospect of reading and writing about science for a living. Soon enough, I was sending off applications to J-schools.

Today, I’m still a kid obsessed with science. I still want to know how everything works.

Tell us a little more about your career trajectory so far: interesting projects past and present? What is taking up the most of your time and passion these days? What are your goals?

After a hard news-intensive graduate program and a couple of internships with local newspapers, I was ready to dive back into science once I had earned my master’s degree. Post-grad school, I worked as a Web intern for the journal BioTechniques, where I covered a variety of life science news and got my first experience writing long-form features on topics like open science, database annotation, and federal funding trends.

Now, at GenomeWeb, I produce both hard news and more in-depth features on genomics research, policy, intellectual property, and more. One of the greatest perks of the job is traveling to conferences to soak in the newest research, attempting to digest all of the advances in a fast-paced field. It’s an exciting time in genomics, to be sure. There’s never a shortage of great science to bring up at the dinner table, nor of great science that should probably never be brought up at the dinner table (here I more or less refer to fecal microbiota transplants, which by the way, I find fascinating).

Speaking of gut flora, microbiome research is a current interest of mine. I look forward to putting my academic studies in clinical nutrition to use for future reporting endeavors on advances in that field.

What aspect of science communication and/or particular use of the Web in science interests you the most?

It has been great to track what the ‘net has done for things like DIYbio and citizen science, and it will be interesting to see what it does for those and similar projects in the future. I’m also really interested in online education and outreach — specifically, how to engage children and foster an early interest in science.

How does (if it does) blogging figure in your work? How about social networks, e.g., Twitter, Google Plus and Facebook? When and how did you first discover science blogs? What are some of your favourites?

Blogging is now part of my day job, but reading blogs has always been indispensable to me as a science writer. Increasingly, social networking is becoming a critical part of my job, as well — primarily through Twitter (I’m new, but have been tweeting on behalf of GenomeWeb, here, here, and here for some time).

Before I began blogging, myself, I followed several science blogs, many of which I still check daily. I’ve also had the privilege of meeting the talented scientists and journalists behind some of those blogs through events like Science Online, society meetings, scientific conferences, and the like.

As a journalist, I also like to keep a close eye on projects that focus on the future of media — scientific and otherwise. The Knight Science Journalism Tracker, the Nieman Lab, and Jay Rosen’s Twitter feed are representative of my go-to sources for such.

What was the best aspect of ScienceOnline2012 for you? Any suggestions for next year? Is there anything that happened at this Conference – a session, something someone said or did or wrote – that will change the way you think about science communication, or something that you will take with you to your job, blog-reading and blog-writing?

I have to say, it took me a few days to fully deconstruct all that I’d heard and experienced at #Scio12, both in and out of the sessions. And then David Wescott came out with this post, describing his “conflicted take,” which really resonated with me.

That some scientists face a lack of support when it comes to communicating their work was not necessarily news, just something I had never really given much thought before.

There was some talk about how to support scientists who wish to communicate their work in the comments at David’s post and in parallel discussions on Twitter, and several pitches at the Scio13 planning wiki appear to accommodate that need. I look forward to participating in those discussions in person come January, online in the meantime.

With that said, it never ceases to amaze me how much time truly smart people are willing to give me to explain their science and the issues surrounding it. Chatting with remarkably talented researchers is, by far, the greatest part of my job, and I could not be more thankful for it.

Thank you for the interview. Hope to see you next year!

Today my guest is Kate Prengaman (homepage/blog, Twitter).

Welcome to A Blog Around The Clock. Would you, please, tell my readers a little bit more about yourself? Where are you coming from (both geographically and philosophically)? What is your background? Any scientific education?

Hi! Thanks for having me! Right now, I’m writing to you from Madison, Wisconsin, where I am working on my MA in science journalism. Although I’ve been interested in a science writing career for awhile, last year was the year I finally decided to put my goals into action, come back to school, start blogging, making connections, and figuring out where I want my future to take me.

Tell us a little more about your career trajectory so far: interesting projects past and present?

Well, I have a BS in Biology and Environmental Science, and I worked for a few years as a field botanist on a bunch of different projects; from endangered species demography in Florida to vegetation mapping of national parks in Alaska and the Mojave desert. Since I returned to school, I’ve been writing about ecology and conservation (my passions) but also about technology, energy, mental health, and food. I’m really fortunate to be working as a research assistant for Deborah Blum as well.

Currently, my coolest project is working with cartography and data visualizations. I used to do a lot of data management and technical mapping (GIS) for my previous job, and I was excited to discover that those skills carry over into science communication. So, I am teaching myself to use Tableau (a data visualization software program) and build maps that tell stories. It’s really fun.

What is taking up the most of your time and passion these days? What are your goals?

Right now, my primary goal is navigating though the world of science writing to figure out where I want to take my career. There are so many more options and opportunities in this field that I had imagined, and attending ScienceOnline2012 and talking to people about their work played a huge part in opening my eyes to the possibilities. Beyond that, my goal is to find a way to make a living talking to interesting people about fascinating science, and then telling those stories.

What aspect of science communication and/or particular use of the Web in science interests you the most?

The best part of of the online science communication community is that it’s truly a community. I’m very new, but it’s inspiring to see so many smart and funny people discussing all kinds of science and its implications across the web. Personally, I am especially excited at the moment to be learning how to use the interactive potential of the web to create ways for people to truly experience information, like the Tableau program I mentioned earlier. I’m so excited, in fact, that I just moved to a self-hosted website so that I could incorporate these graphics I’m learning to make into my blog.

How does (if it does) blogging figure in your work? How about social networks, e.g., Twitter, Google Plus and Facebook? Do you find all this online activity to be a net positive (or even a necessity) in what you do?

As a beginning science journalist, I feel like blogging a great way to get my name out there and a great place to explore and develop my own writing. Although I was initially a skeptic, I must admit that I love twitter. I follow all of the journalists that I admire, and all day long, my twitter feed is full of excellent science writing, interesting news, and occasionally, cute baby penguins in sweaters. I try to limit my twitter access when I need to focus, but I check in throughout the day.

When and how did you first discover science blogs? What are some of your favourites? Have you discovered any cool science blogs by the participants at the Conference?

This is hard to admit, but I didn’t really follow any science blogs until I started graduate school last year. In my defense, I spent most of my time living in the desert with a tent and no cell reception, so I just didn’t have much time to read online. I would read the NYTimes every time I checked back into civilization, and that was it. I read a lot of science books, though. Now, I’ve done a 180, I have so many favorite science blogs that it’s hard to choose. I love the literary voice and strong story-telling at The Last Word on Nothing. I think Superbug is a great example of how many stories you can find, even on a relatively narrow topic. I’m a bit afraid of specialization, but I appreciate that example of how to do it so successfully.

What was the best aspect of ScienceOnline2012 for you? Any suggestions for next year? Is there anything that happened at this Conference – a session, something someone said or did or wrote – that will change the way you think about science communication, or something that you will take with you to your job, blog-reading and blog-writing?

For me, the best aspect of ScienceOnline2012 was how open everyone was to talking about their experiences, positives and negatives, as well as just the extreme amount of friendliness. I went only knowing my adviser and one classmate, and came home knowing so many amazing people. In some ways, it’s made my life harder, I have more blogs to read and more tweets is my feed sharing more awesome things to read, but overall, it’s just been so inspiring. It makes me want to be better at what I do, so I can be a better part of the ScienceOnline community in the future.

Thank you for the interview. Hope to see you next year!

EVOLUTIONARY PHYSIOLOGY OF BIOLOGICAL CLOCKS

“Circadian clocks allow organisms to predict, instead of merely react to, cyclic (predictable) changes in the environment”. A sentence similar to this one is the opening phrase of many a paper in the field of chronobiology. Besides becoming a truth by virtue of frequent repetition, such a statement appeals to common sense. It is difficult to imagine a universe in which it was not true. Yet, the data supporting the above statement are few and far-between. Believe it or not, the data are not always supporting it either.

This post will attempt to briefly review the literature on evolutionary and adaptive aspects of biological rhythmicity. Also, using the perspectives and the methodology of evolutionary physiology, I will try to suggest some ways to test the hypothesis stated in the first sentence above.

REASONING BEHIND THE ARGUMENT FROM COMMON SENSE

For outside observers of the field of chronobiology and its recent successes in molecular, neural and medical aspects of biological rhythmicity, it may come as a surprise that the field was founded by ecologists, ethologists and evolutionary biologists. When the statements about adaptive function of clocks were initially made, the authors were much more careful than is usually seen today. It was meant as a hypothesis to be tested, and elaborate reasoning was often offered to persuade the reader why it might be true (Daan 1981, Pittendrigh 1967,1993, Enright 1970).

One of the most common arguments that a clock must be adaptive (for one reason or another) was its ubiquity – all plants, fungi, protista, invertebrates and vertebrates (more recently cyanobacteria, too) tested by the pioneers in the field showed circadian rhythmicity. The way those rhythms behaved in the laboratory in various experimental treatments was surprisingly similar over all species. Thus, the reasoning goes, if a physiological mechanism is found in every living thing, and it seems to work in the same way in all of them, then it must have originated early due to natural selection and was preserved over eons due to natural selection.

Some of the earliest experimental work was designed to test the genetic basis of biological rhythmicity. Many generations of laboratory organisms were raised and spent all their lives in aperiodic environments, yet the rhythms persist (Sheeba et al. 1999). Period of the rhythm was species -specific, highly heritable, and very amenable to artificial selection. So, if it is in the genes, the clock must have evolved due to some kind of selective pressure.

When reviewing evolutionary literature on biological rhythms, it is often difficult to distinguish between hypotheses of current utility from hypotheses of origin. It was often assumed that same selective pressures which keep the clocks ticking all over biosphere today, are the pressures responsible for the initial discovery of timing mechanisms by early forms of life.

The current adaptive functions of biological rhythms are often divided into two, mutually not exclusive categories. The Internal Synchronization hypothesis stresses the need for temporal separation of incompatible biochemical and physiological processes within a body (or cell), and for temporal synchronization of processes which need to coincide. An example of the former would be temporal separation of photosynthesis from nitrogen fixation. For the latter, surge of a hormone and availability of its receptor need to be synchronized for the generation of the endocrine effect. Evolution of such timing control mechanisms would presumably alleviate energetic costs of constant production of enzymes and their substrates.

The External Synchronization hypothesis supposes existence of temporal niches. For instance it would be adaptive for an animal to forage at the time when food is available, to hide when the predators are hungry, and to find an individual of the opposite sex at the time conducive to mating. Notably, it was never explicitly stated that possession of a clock is adaptive only if everyone else has a clock, too. So, who had it first?

The two hypotheses are easily meshed. A bird will sleep instead of foraging while its body temperature is low. It will wake up, raise its temperature and corticosterone levels and start to forage when the conditions outside are most conducive to it – when it’s warm, light and worms are crawling around. The old adage about the early bird getting the worm is often invoked (and, as R.A.Heinlein once quipped, “it just goes to say that the worm should have stayed in bed”).

Coupled to the second hypothesis is also the notion that circadian clock is involved in temporal memory (Enright 1975, Biebach et al. 1991). Thus every event which is committed to memory will, along with information about “what” and “where”, also have a time-stamp given by the clock – the “when” of memory. If doing something at one time of day yesterday resulted in survival it might be prudent to do it again today at the exactly same time (Daan 1995).

One important distinction between the origin of the first clock and its current use is in the size and complexity of the organisms in question. The first clock presumably appeared in a unicellular organism. Most of the research today focuses on multicellular organisms.

In the first case, we are talking about a single-cell clock, in the second about the circadian system, which may be composed of many clocks of different properties, all interacting with each other, with the environment, and with other functions of the body. There is only so much a single cell can do. A complex clockshop which exists at a higher level of organization can evolve complex new functions, e.g., photoperiodic time measurement, time-compensated sun-compass orientation, tidal, lunar and circannual rhythms.

In the study of evolution of biological rhythms, are we talking about evolution of the cellular building blocks or evolution of higher-order systems?

CHRONOBIOLOGY IN THE CONTEXT OF EVOLUTIONARY PHYSIOLOGY

The 2000 review of Evolutionary Physiology by Feder, Bennett and Huey currently serves as a manifesto of the field (Feder et al. 2000). In this section, I will follow the organization of their paper to explore how circadian physiology might fit into the framework of evolutionary physiology, as well as how evolutionary approaches may benefit the study of biological rhythms.

Evolutionary physiology is a relatively recent natural outgrowth of the field of comparative physiology, which, in turn, developed out of general mechanistic physiology. The evolutionary physiologists are direct intellectual (and often academic) descendants of traditional comparative physiologists, so the topics remain similar: scaling, symmorphosis, as well as studies of metabolism, respiration, osmoregulation, thermoregulation and locomotor performance. However, other aspects of physiology have been tackled by other groups of scientists, e.g., comparative endocrinology, neurobiology, sensory physiology, digestive physiology and reproductive physiology are vibrant fields of their own. Comparative chronobiology has a long tradition, too (Horton 2001). The importance of comparative studies to understanding of underlying mechanisms can be seen from examples of medically driven areas of physiology (e.g., sleep). Such areas fumbled in the dark for decades due to lack of basic understanding of what the process is all about, which in turn was due to lack of comparative studies of the phenomenon within an adaptive and evolutionary context.

It would be erroneous to state that evolutionary thinking was not a part of physiological thinking in the past, yet evolutionary physiology explicitly imports evolutionary theories, paradigms, concepts, models and techniques into the study of physiological adaptation. Feder et al. (2000) recognize four major developments which led to the rise of evolutionary physiology out of its general and comparative precursors.

First, the critique of adaptationist thinking (Gould and Lewontin1979) had an enormous ripple effect through all of biology, including physiology. The naive assumption that every trait is an adaptation forged by natural selection gave way to a more sophisticated view of evolution that includes non-adaptive forces like constraints and drift. Here, the ubiquity of biological clocks and the inability to imagine a clock-less universe led to the common view that not just the sheer existence of the clock, but every aspect of its mechanism must be an adaptation to the environment which evolved through the agency of natural selection. The non-adaptive evolutionary mechanisms are difficult to fathom in this context, and no explicit statements were made in the literature along these lines.

Second, new awareness of non-independence of species as analytical units for comparative biology has resulted in development of new analytical tools, new approaches to comparative studies, and, most importantly, in the shift in emphasis to ancestor-descendant relationships. Comparative studies of biological clocks were the foundation on which the whole field of chronobiology was built. Yet, these studies were not explicitly phylogenetic. The clocks are so widespread that comparisons were rarely made between closely related species. It was, and still is, more common to compare representatives of plants to fungi to insects to mammals. On those rare occasions when a phylogenetic tree appears in chronobiological literature, it is most likely to be the Tree of Life and not just a tiny piece of it. Thus, the non-independence of species is a problem that did not have much impact on comparative work to date, but is one that will have to be tackled in the future when more analyses of closely related species are performed.

Third, incorporation of tools of evolutionary biology into physiology allows research to state evolutionary hypotheses a priori, instead of post hoc. Using these tools, one is able to monitor evolution in progress and predict future evolutionary trajectories, instead of just registering the results of past evolution. In chronobiology, a few studies have recently been performed along these lines, more concerned with photoperiodic than circadian time-measurement, though (Ben Saad and Maurel 2001, Heideman et al. 1999, Heideman and Bronson 1991).

Fourth, use of most recent tools of molecular biology allows one to escape from standard genetic laboratory models to many other species of interest to physiologists. Comparative molecular analyses of genes involved in circadian rhythmicity have been performed in Diptera and Lepidoptera, and work on other organisms is sure to follow in the near future (Piccin et al. 2000, Peixoto et al. 1998, Costa and Kyriacou 1998, Kyriacou et al. 1996, Saleem et al. 2001).

Evolutionary biology aims to answer two kinds of questions: about the process (“how evolution works”) and the pattern (“what has evolution wrought so far in the history of life on this particular planet”). Evolutionary physiology, as its subset, is likewise interested in both process and pattern. After all, one informs the other and vice versa. In the same vein, mechanistic and evolutionary data inform each other and vice versa, too. While traditional comparative physiology explained mechanistically how the organisms adapt to their environments and added adaptive explanations post hoc, the modern evolutionary physiology starts with evolutionary predictions and tests them with comparative studies in the laboratory and in the field.

Of particular interest is the question of optimality – is there a close match between requirements of the environments and the physiological answers to these, or are safety margins and overdesign the rule. It would be difficult to define what would safety margins and overdesign mean in the field of circadian clocks. The clock is at the very core of physiological function of an organism. It acts as a relay station which controls practically every other aspect of biochemistry, physiology and behavior. It is not expected that the cellular clock at the core will be much affected by the environment, but the outputs of the clock, the signals from the clock to all the other functions, are much more likely to be the target of selection. Plasticity of the circadian system and of its coupling to downstream functions is a trait that can be expected to correlate to environmental parameters, e.g., stability vs. variability of the environment.

EVOLUTIONARY CRONOPHYSIOLOGY TO DATE

Several approaches to study of evolutionary pattern and process have been employed by students of biological rhythms. These include studies of variation in natural populations, including latitudinal clines (Skopik and Takeda 1987, Sawyer et al. 1997), tests of correlated traits, e.g., circadian vs. photoperiodic (Majoy and Heideman 2000) or circadian vs. developmental timing (Bloch et al. 2001), and studies of responses to artificial selection.

Comparative studies have been performed on levels from molecular to organismal. However, the choice of species is questionable. If relevant environmental parameter is the light-dark cycle, then most species studied so far occupied the same environmental niche – the earth surface in a temperate region. For a comparative study to be able to discriminate between ecological specialization and phylogenetic inertia, one needs to compare organisms occupying different environments. In the case of clocks, such environments would include polar regions (light-dark cycle of LD 6mo:6mo), equator (constant LD12h:12h), and life below the surface (constant darkness, DD). Although many species have been studied in such conditions in the lab, the study of organisms that live in such conditions in the wild is rare. Recent studies on subterranean and cave animals are a welcome change to the comparative work in chronobiology (Lee 1969, Hoenen and Gnaspini 1999, Riccio and Goldman 2000a, b, Avivi et al. 2001, Koilraj et al. 2000, Trajano and Menna-Barreto 2000).

Most recent data on adaptive function of circadian clocks employed measurements of fitness in altered light environments, as well as comparisons of fitness between genetic mutants of clock function. However, the only measure of fitness used is longevity (Pittendrigh and Minis 1972, Klarsfeld and Rouyer 1998, Hurd and Ralph 1998), and only two papers look at the trade-off between longevity and the lifetime reproductive output (Sheeba et al. 2000, Beaver et al. 2002).

Phenotypic engineering is the hallmark of studies by Patricia DeCoursey, one of the pioneers of the field (DeCoursey et al. 1997, 2000, DeCoursey and Krulas 1998). She measures survival of various species of rodents in the wild after she has removed their circadian pacemakers in the suprachiasmatic nuclei of the hypothalamus. The data are not as straightforward as one might expect – the survival is dependent on how bad was the year in regard to abundance of predators. Masking effects of light on behavior, i.e., burrowing during the day due to bright light, can protect clockless animals from predation in some cases, dependent on the species of rodent and the species of predator. There are two main problems with these kinds of studies. First, the effect of removal of the clock is observed in only one generation. If some clock-less individuals managed to survive and reproduce every year, and if it was engineered (genetically?) in such a way that the progeny were also clock-less, would such a population manage to establish itself in the wild? What alternative mechanisms it would evolve to decrease risk from predation? Would other correlated aspects of timing (e.g., photoperiodism, developmental timing, ultradian rhythms) additionally reduce their fitness? If we are removing a mechanism that was inherited for billions of years, why would we expect that an alternative mechanism would exist to protect the animals in the absence of the clock?

FINDING THE CORRECT ECOLOGICAL CONTEXT FOR EVOLUTIONARY CHRONOPHYSIOLOGY

Earlier in this post I noted that most of the thinking about adaptive function of biological clocks concentrated on adaptation to physical environment – the daily rhythm of light and darkness. That is quite reasonable assumption when one is concerned with the original appearance of a biological clock in the primordial soup, and might still be valid in studies of some unicellular organisms (Dvornyk et al. 2002). Yet, in a world of today, in which it seems that everyone’s got a clock, it seems reasonable to assume that biotic aspects of the environment would be the key selective pressure for current uses of biological timing mechanisms. Thus, studies of temporal aspects of interactions between individuals, groups, populations and species can potentially provide important insights into the evolution of biological clocks. That kind of research would also be forced into further sophistication. Many biotic interactions are dependent on niche-constructing traits, as well as on traits that evolved due to simultaneous selective pressure at two or more levels of organization, e.g., genic, individual and group selection acting at the same time either in the same direction, the opposite direction, or at some angle between the vectors.

Several exciting research findings along these lines of thought have been reported recently. First, in 1998, the “resonance hypothesis” was tested in cyanobacteria by Carl Johnson’s group at Vanderbilt University. The notion that intrinsic (“freerunning”) period of the circadian clock needs to be similar to the period of the entraining cycle (24 hours in nature) was tested in period mutants of Synechococcus sp (Ouyang et a. 1998). Various mutants were exposed to different lengths of the light cycle. Two mutants were tested at the time in competitive assay protocols. In every case, the strain with intrinsic period more closely matching the entraining period won the competitive assay. Thus, being in sync with the environment confers fitness against conspecific competitors (Johnson et al. 1998).

A series of papers appeared recently on temporal niche exclusion between two con-generic species of golden spiny mice living in sympatry in Israel. Originally both nocturnal, in the area of sympatry one of the species adopted a diurnal lifestyle. Physiological adaptations to diurnality, including thermoregulation, osmoregulation and vision, were not altered. The circadian performance in the laboratory was not different either. The only difference was in the coupling between the clock and the behavioral output (sleep-wake cycle) in the field, i.e., detachment of the activity rhythm from circadian control under the ecological pressure of competitor’s presence (Kornfeld-Schor et al. 2001).

Fleury et al (2000) tested the hypothesis that the least competitive parasitoids of fruitflies would gain adaptive advantage from parasitizing their hosts earlier in the day than their competitors. Comparison of three species of parasitoids in the lab and field revealed that this indeed is the case, as well as that the time-of-day of parasitism was directly driven by the properties of the circadian clock in each of the three species (Fleury et al. 2000).

III. Whence Clocks?

Origin, Evolution, and Adaptive Function of Biological Clocks

The old saw about the early bird just goes to show that the worm should have stayed in bed. (Heinlein 1973)

Now darkness falls.
Quail chirps.
What use Hawk eyes?
(Basho)

Local/temporary and global/universal environments.

In the study of adaptive functions, usually the question is asked about a function A in the species X. This implies that the species X has evolved the function A as a response to recently and currently selective local environment a. One then studies the pertinent aspects of the environment a, the function A of X in the field and in the lab, and, perhaps, the similar function A2 of a similar species Y in the similar environment a2.

However, not all adaptive functions are adaptations to local environments. Some aspects of the environment are global. All organisms on Earth are adapted to its gravity. It can be safely assumed that even the first life form on the planet had this adaptation. Some environmental factors are global now but might not have been throughout the history of the planet, like the proportions of oxygen, nitrogen and other gases in the atmosphere. Some adaptations are very frequent although they do not seem to have a correlate in the external environment – for instance sexual reproduction. Such adaptations are result of the particularity of the mechanisms of evolutionary change on Earth, and might not have evolved if the life on Earth initially adopted different mechanisms of evolution. Other adaptations are correlated with an environmental factor which is global for a large number (but not all) of very diverse organisms, e.g., the properties of the marine environment.

Temporal structure of the environment.

Movements of the Earth, the Moon, and the Sun in relation to each other, and the rotation of Earth around its tilted axis, have tangible effects on all organisms inhabiting surface, or near-surface, habitats of the land and oceans of the planet. Only deep-soil Archaea, and the deep-oceanic organisms may conceivably escape from all the astronomically generated rhythms of the Earth’s surface: daily cycle of light and darkness, the phases of the moon, the tides, and the seasons of the year.

The common properties of all these cycles are their precision and regularity – they are highly predictable. Organisms cannot evolve adaptations to rare and unpredictable events (e.g., meteor impacts), but can easily adapt to predictable and rapid cyclic events in the environment (Bornemisza 1955).

Why would organisms need to adapt to the natural cycles? In short: because they need to adapt to their environments, and the effect of the cycles is that each organism needs to adapt to more than one environment. For a rabbit, a meadow is a single spatial environment. However, it comprises of a number of temporal environments. The meadow by day and the same meadow at night are two very different worlds. If we multiply that with four seasons (spring, summer, fall, and winter environments) and at least two extreme values of intensities of moonlight at night, we arrive at the conclusion that the rabbit needs to adapt to twelve different environments!

All these cycles have been quite stable throughout the history of Earth. The alteration of night and day affected even the simplest unicellular organisms which were the only inhabitants of the planet for most of its history, as they rely on sunlight as the source of energy for metabolism and replication. As the organisms grew bigger, lived longer, and invaded other environments, longer cycles gained in importance, too. Seasonal changes in daylength are substantial towards the poles, and the annual changes in weather conditions are quite dramatic around equator.

Adaptations to environmental cycles.

What are the possible ways an organism may adapt to temporal changes? Certainly, an organism may use its sensory mechanisms to behaviorally react to the changes as they happen. When the sun comes up in the morning, the animal perceives the light and the warmth, wakes up and goes out to forage (or goes into the burrow to sleep). When nice weather and plentiful food arrive in spring, the animal mates and raises its young. In principle, this arrangement could work, as each species would evolve its own time-table of stimulus-responses to cues.

However, the extremely predictable changes are a form of information, and information is an important resource as it creates opportunities which can be exploited. It can be advantageous to an organism to be able to predict the changes before they occur. If a bird lets its body temperature drop while sleeping at night, and starts warming up at the crack of dawn, it will take some time, perhaps an hour or two, before its temperature is optimally high for foraging and predator avoidance. Another bird which can predict the time of dawn can start raising the temperature while it is still dark outside. At dawn, it is ready to go – the early bird gets the worm! The early bird leaves progeny – the other one goes extinct.

Another avian example: One bird saves the energy by keeping its reproductive system regressed during the winter. When spring brings nice weather, this bird grows its gonads, a process which takes a couple of weeks (longer in mammals). When the reproductive system is ready, provided the potential mates have also reacted the same way, the bird mates, lays eggs and raises hatchlings.

Another bird predicts the coming of spring by measuring the lengthening of the daylength (photoperiod). On the first day of nice weather, the bird is ready to mate. This bird is not wasting the first couple of weeks of bountiful food and warm air. A few weeks later, her chicks are out foraging and outcompeting the younger, smaller chicks of the first bird. The second bird can also expand its range towards the poles, as it can perform the whole reproductive effort within a very short window of opportunity, while the first bird would lay the first egg at the time when the bad weather has already returned.

It is obvious I love birds, so let me indulge in another avian example. As the winter gets closer, but the weather is still nice and the food abundant, a bird measures the shortening of the photoperiod and anticipates that the weather will change. She stops her reproductive effort early, she puts on large fat reserves, shrinks many internal organs, drops her old tattered feathers and grows new, healthy, and not so sexually attractive plumage. She gets together with other conspecifics of the area who were, up till then, fiercely territorial. Together they undergo a period of a flying exercise and fitness program. At a particular day of the year, the whole flock heads south to the distant warm winter feeding grounds. On their way there, the birds use the position of the sun to orient. The position of the sun changes during the day, but as these birds have the sense of time, they can compensate for the sun’s movement across the sky, and will not get lost on the way. They will use the same methods to prepare for, accurately time, and precisely retrace the route on their flight back home in spring. Another bird which passively responds to the environment will stay at home until the first frost and will freeze together with her last clutch of newly-hatched chicks. If she attempts to migrate, she will have to do it alone, with no preparation, with insufficient energy stores, and with no idea how to navigate to the target environment and back.

Clocks as adaptations.

The competitive advantages of having an internal anticipatory system have played a role in the evolution of biological clocks (Pittendrigh 1965, 1967, 1993, DeCoursey 1990). Daily biological clocks, or circadian clocks, are endogenous, inherited timing devices which control rhythms of many physiological and behavioral functions. The clock can time changes in a variety of processes at any time of day that is advantageous to the organism, as well as translate the daily changes into rhythms with longer or shorter periods. The clocks, being organic structures, are not absolutely precise, so they have evolved the means by which external timing cues, like dawn and dusk, can entrain the phase of the clock to the local time.

The possession of the internal timing mechanism will also allow the organisms to invade novel ecological niches, e.g., polar regions, intertidal regions, migratory way of life, etc. As the predators and prey evolve biological clocks, the selective pressure on other organisms to do the same increases even more, as the biotic aspects of the environment get even more temporally complex in even more selectively meaningful ways. This may lead to coevolutionary arms-races around the circadian clock, as a predator tries to invade and the prey to escape a particular temporal niche. Unlike other arms-races, this kind will not lead to runaway selection of novel traits, as the clock is a closed loop (they may chase each other in circles forever). However, this may lead to an adaptive trend towards greater sophistication and flexibility of the timing mechanisms, including multi-oscillator systems, clocks modulated by the internal states, circannual clocks, etc.

The function of the clock in adaptation to the temporal changes in external environment is not its only function. Another hypothesis exists which states that one of the important roles of the timing mechanisms is the internal coordination of physiological and metabolic functions. Some cellular and organismal processes are incompatible with each other. If there is no possibility that two processes can be segregated spatially, then their temporal isolation is the only remaining solution. Theories differ in assigning relative importance to the two functions, and in stating which function arose in evolution first (Winfree 1990, pp.387-394, Edmunds 1988, pp.368-370, Pittendrigh 1961,1967, 1981, 1993, Enright 1970, 1975).

Another hypothesis is that the circadian clock is the organ of the sense of time (Daan 1995, Enright 1975). Unlike other sensory modalities, the clock does not respond to any form of energy from the environment. It measures the passage of time internally, and gives the non-directional physical time a direction (“arrow”) by virtue of being in a living organism (Frazer 1996). The clock is, thus, an internal representation of time, a cognitive temporal map analogous to the cognitive spatial maps. This allows the organism to perform interval time measurement, distinction between before and after, measurement of duration of events, and learning of the local time of day (Shettleworth 1998, pp.333-378.). Presumably, only this last function requires that the clock, indirectly via other sensory modalities, be entrained to the local time.

Origin of timing mechanisms.

There are three main lines of thought concerning the origin, evolution and adaptive function of biological clocks (Winfree 1990). The first view assumes that in the beginning the organisms were arrhythmic. The cyclic nature of energetic availability and cycles of potentially degrading effects of the sun’s ultraviolet rays on particular pigmented enzymes, provided the selective environment. A cell with a timer can predict the changes and adjust its metabolic activities to minimize energetic and material loss. This cell will outcompete the other cells in the Archeozoic sea (Pittendrigh 1967). The emergence of such a system so early in the evolution of life leads to prediction that the molecular mechanisms of circadian rhythmicity will be highly conserved among all organisms (Winfree 1990, p.389).

The second view assumes that the environment itself forces rhythmicity onto the early unicellular organisms (Goodwin 1966). To economize waste, the cell evolves modifier genes. Each of these gene products will have a role in facilitating a smooth transition from one to the next phase of the imposed cycle. As more and more such genes evolve, every state of the cycle comes under genetic control. Three billion years later “the cell might surprise itself to discover…when some scientist first puts it into constant conditions, that it shuffles its way spontaneously through almost the same cycle” (Winfree 1990, p.390). So, even though all the cogs and wheels were, the whole clock itself was never selected for.

The third view states that all biochemical processes are cyclic. Furthermore, this cyclicity is part of the definition of life. Some of the cycles are regular, and the periodicity of such oscillations can be modified by natural selection (Winfree 1990, pp.391-392). Flexibility in counteracting stabilizing homeostatic mechanisms can add another degree of freedom in which to search for optimization. The second and third views expect to see almost as many circadian mechanisms as there are species. If one speculates that the life originated in the shallow tidal pools, than the circatidal rhythms might have been the first to arise, either before or simultaneously with the circadian clocks.

There is nothing incompatible between the three views. They could have conceivably all contributed to the emergence of timing mechanisms. However, neither one of them explains why was it that a self-sustaining clock evolved. Why does a circadian rhythm persist in constant conditions for many days, months and years? The organisms were selected only for ability to cycle in a regularly cycling environment. Why is the clock not an hourglass mechanism which can be turned over by the environmental cues every day? Enright (1970, 1975) suggests that role of the clock in acquisition of temporal memories might have had an influence. Aschoff (cited in Enright 1970) suggested that an oscillator which is capable of a small number of cycles will be adaptive in times of weather catastrophes, during hiding and burrowing, and during hibernation. Such a timer, by virtue of capability for a few oscillations, inevitably can cycle indefinitely.

Comparative method in the study of clocks.

As temporal structure is a property of a global environment, the study of the mechanisms of time measurement will depend on our understanding of the origin, evolution and adaptive function of circadian clocks. Should we expect a mechanism as conserved as glycolysis, or use of ATP for energy, or mechanism of DNA transcription? Or should we expect that every narrow group of organisms has evolved a different mechanism? Or something in between? And how do we study the clocks in order to distinguish between phylogenetically conserved generalities and the ecologically determined novel particularities?

Comparative method is a “range of techniques that infer how one organism evolved by comparing what evolution produced in that case with what it produced in other cases…The comparative method… has three important applications… First, it enables us to directly test the historical assumptions tacit in adaptationist hypotheses. Second, it enables us to test the proposed link between environmental feature and adapted trait. Third, we can use it to make sense of the adaptationist claim about the explanatory priority of selection” (Sterelny and Griffiths 1999, pp.243-244).

An adaptationist hypothesis (e.g., about the adaptive function of the circadian clock) can be tested by checking the actual sequence of evolutionary changes to see if it is the one presumed by the hypothesis. A hypothesis may propose that a particular trait arose before another trait (e.g, hourglass before clock, circadian before circatidal rhythm, single before multi-oscillator systems, etc.). The hypothesis can be tested by comparing the traits in earlier and later representatives of a lineage (in the case of clocks as responses to a general feature of the environment – the entire tree of life).

Comparative method can also directly test the adaptationist hypothesis that adapted traits are responses to particular features of the environment by measuring if there is a tight correlation between a particular environment and a particular trait (e.g., are the deep-oceanic creatures, or cave and subterranean animals arrhythmic; is there a correlation between degrees of robustness of the circadian amplitude and the stationary vs. migratory habit, or burrowing vs. open field habitat).

Adaptationist extremist position is that convergent evolution illustrates the overwhelming power of natural selection over all other evolutionary mechanisms (genetic drift, sexual selection, etc.). But, convergence tells us nothing about the relative powers of selection and history unless we can somehow count all the possible convergences that have not happened – all the times history “won”. Is a presence of a trait in a number of organisms the result of convergent evolution? This can be answered only by extensive use of comparative method. One cannot know if something is a convergence without a phylogenetic tree. If analysis of the tree reveals that the trait appeared repeatedly de novo, than it is a convergence and the force of natural selection is a primary explanation. If analysis of the tree reveals that all members of a lineage posses the trait, than it is not a convergence. The trait was probably adaptive for the common ancestor, but it might not be adaptive at all today. It could still be an adaptation as it may serve many different adaptive (exaptive) functions in different species and exist merely as phylogenetic inertia in others.

The adaptive hypothesis requires that the clock be phase-shiftable by an environmental cue and that it be temperature compensated. These are the two absolute requirements for its proper function. Every timing system will satisfy these minimal requirements no matter what the underlying mechanism may be. So, these two properties cannot be informative about the mechanisms, and if “we are to test the proposition of a common mechanism and use only formal properties, these must be of such a nature that selection can reasonably be dismissed as the agent responsible for their universal association with cellular clock systems; in short, the properties must lack adaptive value” (Pittendrigh and Bruce 1959) and the “study of features which do not seem to have any survival value…may be indicative of the structural properties of the system” (Pavlidis 1971).

So, is the circadian clock a universal adaptation, a case of convergent evolution, or a generatively entrenched relic of history? Here, one needs to make a sharp distinction between the circadian clock which is the timekeeping molecular mechanism in a single cell, and the circadian system which includes all the cellular clocks, all the sensory input pathways to the clocks, and all the mechanisms of translating clock states into overt rhythms of a whole organism (Underwood et al. 1997a). A clock is a molecular mechanism, while a system uses the molecular mechanisms to produce overt rhythms.

Circadian systems.

Data so far indicate that all the biological rhythms studied to date possess the basic properties of entrainability and temperature compensation. I have collected literature on observations and experiments in hundreds if not thousands of species of unicells, plants, fungi and animals, but the limitations of time and space prevent me from presenting them all in this abstract, so I will have to leave them for a later publication. All timing systems can be brought to match the local time, and will do so in a precise manner over a range of temperatures (if they could not they would be thermometers, not clocks). Temperature compensation varies with latitude in fruit flies (Sawyer et al. 1997). Critical photoperiod for induction of reproduction in mammals and birds, as well as the number of eggs in a clutch in birds, both traits regulated by the circadian system, correlates with latitude in many species (Baker 1937, 1938a,b., Daan and Aschoff 1975, Bronson and Heideman 1994). This indicates that the circadian clock (and all other circa-rhythms) is an adaptation, as the trait tightly correlates with the environment.

It is interesting to note that many organisms which live in caves and under ground still have circadian rhythms. For instance, Mediterranean blind mole-rats have circadian rhythms entrainable by light (David-Gray et al. 1998), as do the natural or induced disperser phenotypes of the African naked mole-rats (Goldman 1999, contrary to Davis-Walton and Sherman 1994). Cave-dwelling crickets have circadian rhythms which are nor entrainable by light, but by noise/silence cycles (Marques and Hoenen 1999).

Cave-dwelling catfish are apparently arrhythmic, but a rhythm emerges if the fish are exposed to a light-dark cycle (Trajano and Menna-Barreto 1999). Overt behavioral rhythmicity is dependent on intensities of light and levels of temperature in Japanese Newts (Nagai and Oishi 1999) and Leopard Geckos (Chris Steele, unpublished data). These data suggest that circadian systems in these organisms are “rudimentary organs” which were not entirely lost during the course of evolution from their surface-dwelling ancestors. Alternatively, one can argue that the clocks persist in these organisms due to their utility in orchestrating myriads of physiological events within the body, and that the persistence of a behavioral output is just a left-over from the past.

Some emergent properties of circadian systems are lost only to reappear again and again when the need for them arises, presumably because it is relatively easy to re-invent them since all the clock parts are already present. For instance tidal rhythms have been found in birds and lizards (Daan and Koene 1981, Sawara et al. 1990, Wikelski and Hau 1995). Lunar cycles appear in some terrestrial species of plants, invertebrates, mammals, birds and reptiles (Abrami 1972, Skutelsky 1996, Brigham et al. 1999, Chris Steele, unpublished data).

Circadian rhythmicity does not disappear in artificially imposed relaxed selective environments. After 600 generations in constant conditions, fruit flies retain precise circadian rhythmicity in behavior and pupal eclosion (Sheeba et al. 1999) suggesting that rhythmicity is important in regulating cyclic biochemical processes within an individual fly, as much as in proper phasing to the environmental cycles. Similar conclusion can be drawn from the fact that it is easy, by experimental manipulation or by genetic selection, to eliminate behavioral but not physiological circadian rhythms in quail (Guyomarc’h’ et al. 1998, Zivkovic et al. 1999).

Interestingly, it took a long time to discover circadian rhythms in the laboratory Nematode C.elegans. In this animal, the so-called “clock-genes” are present, the ortholog of PER cycles with an ultradian rhythm with a period of about 6 hours and is thought to regulate timing of developmental events (Jeon et al. 1999). The circadian rhythmicity in this animal was not completely eliminated through many generations of laboratory rearing practices, yet the involvement of circadian clock genes in timing of development is apparently compatible with their use for circadian behavioral timing.

Archaea and most Eubacteria are arrhythmic. For Archaea, the explanation might lie in their ecology – they usually inhabit the most inhospitable regions of the planet including deep-oceanic hydrothermal vents, deep soil, rocks, salt deposits, polar regions, underground hot-water springs, where the rhythms of the planetary surface might not have any direct effect on their survival. Some Cyanobacteria have circadian rhythms as they need to temporaly separate incompatible reactions of photosynthesis and nitrogen fixation (Johnson and Golden 1999). Real Bacteria, being Prokaryotes, might just be capable of a rapid response to the direct environmental fluxes, and a timer might impose too rigid a control in, on their scale, essentially unpredictable environments.

Cellular clocks.

Molecular clocks are invisible to selection. Circadian systems, being in direct interaction with the environment, are more likely to show correlations with the environment and a faster rate of change over evolutionary time scales. It is perfectly safe to state that all mammalian systems are built basically the same way, which differs from the avian, reptilian, insect or plant systems. Some data also exists suggestive of correlations between some formal circadian properties and specific ecological niches.

All the circadian systems contain, as their parts, cellular circadian clocks. Nothing a priori dictates that the cellular clocks need to have, or not have, exactly the same molecular mechanisms of rhythmicity. It is conceivable that a cellular clock can be just a rudimentary timer, even an hourglass, and that the multicellular organization of the system provides temperature compensation, and entrainment properties. Also, even if the dynamics of the mechanism are the same, it is not necessary that the actual molecular players remain the same.

What do the actual molecular data show? Each circadian clock cell in all organisms is a self-sustaining circadian oscillator, resettable directly or indirectly by light, and it is temperature compensated (reviewed by Dunlap 1999). The dynamics of the mechanism are very similar in cyanobacteria, plants, fungi, insects and mammals. The molecular clock is a negative feedback transcription-translation-based oscillator in all of the studied organisms. Fungi, insects and mammals use PAS-domain-containing proteins as positive elements. Insects and mammals have pairs or families of negative elements. Several genes can be found both in the fruit fly and in the mouse., e.g., per, tim, clk and cyc in flies have homologs in per1, per2, per3, tim, clock and bmal in mice. Drosophila dbt is a sequence homolog to casein kinase 1.

These are the similarities. How about differences? All negative elements cycle (in expression) in fungi and insects, but only some in mouse. No positive element cycles in fungi, one in the fruit fly and a different one in the mouse. The phases at which elements act are shifted – fungi and mammals have a day-phase clock, while the fruit fly has a night-phase clock – a complete change in internal logic of resetting by light.

So it seems that nature is using some well-conserved themes but is mixing and matching the details. Is there a consensus today about the evolution of circadian function on Earth? Past five years have seen an avalanche of new molecular data. Every few weeks a paper is published, it seems, which leads to a change in one’s opinion on the evolutionary conservatism of the clock. A surprising finding of a similar gene or function in two very distinct organisms points to overall great similarity of mechanisms. Next paper discovers a seemingly unexplainable difference in mechanisms between relatively closely related organisms, and suggests that each species has freedom to tinker with the basic clock mechanism. The field as a whole is oscillating on this issue. If there is anything like a consensus, it is the idea that clock is always running and is full of redundant elements. As long as a wheel or a cog can be removed or replaced without stopping the clock, the overall mechanism will stay the same, although the individual players may, one by one, all be replaced over long periods of evolutionary time.

However, data exist which challenge the notion that transcription/translation loops of clock genes are mechanisms of all aspects of circadian rhythmicity (Hall 1996, Lakin-Thomas and Johnson 1999, Lakin-Thomas 2000). In an alga, Acetabularia, circadian rhythmicity persists in cells from which the nucleus was removed and the transcription of non-nuclear DNA was pharmacologicaly blocked. However, this rhythmicity damps out after several cycles, and re-introduction of the nucleus restarts the rhythm with the phase dictated by the nucleus (Edmunds 1988). These data suggest that the circadian clock in this organism consists of two parts – a nuclear (transcription/translation loop) and a cytoplasmic clock. These two clocks interact with each other. A computer model was developed (Roenneberg and Merrow 1998, 1999) which shows how such a feedback system of two oscillators can account for stability of period, persistence of rhythm in prolonged constant conditions, temperature compensation, resistance to environmental noise, and entrainment properties of the cellular clock.

There are also data suggestive that some of the circadian rhythms are and others are not controlled by the “clock genes”. Null mutations, deletions and continuous overexpression of per gene in fruitflies does not entirely abolish circadian rhythmicity. The behavioral activity rhythms of fruitflies are characterized by two peaks. Evening peak is assumed to be the time when the insects are foraging. The morning peak is the time when the insects are involved in reproductive activities: search, courtship and mating.

Elimination of cycling of PER protein eliminates the evening peak. However, the morning peak persists for several more cycles, then the period gets shorter (ultradian), and finally dissolves into arrhythmicity (Renn et al. 1999, Helfrich-Forster 2000, Gvakharia et al. 2000, Kaneko et al. 2000).

In the giant silkmoth, PER protein never enters the nucleus in the pacemaker cells responsible for overt behavioral rhythmicity. However, it does enter the nucleus in some peripheral tissues (Sauman and Reppert 1996), suggesting that a transcription/translation loop is part of some but not all cellular circadian clocks.

Two separate circadian systems can be observed in female birds of some species. One system, driving rhythms such as locomotor activity, feeding activity, body temperature, oxygen consumption and melatonin release is sensitive to light and melatonin and can be readily entrained to light-dark cycles. The other circadian system drives all the mentioned overt rhythms, but also the circadian rhythm of ovulation and oviposition. This rhythm is not directly entrained by light cycles. It tends to free-run through a portion of the day. As the two systems interact, and as they show two different periods (24h for the entrained system and some other value for the other system), the two rhythms continuously change mutual phase relationships. Some phase relationships are “permissive” and others are “forbidden”. As the ovulatory rhythm intrudes into the “forbidden zone”, its interaction with the other system makes it phase-jump back to the starting (default) phase from which it starts free-running again. Interaction between two clocks may be neural (e.g., between two hypothalamic pairs of nuclei) or hormonal (perhaps sex steroid hormones). The main system consists of the pineal gland, the retinae, and a pair of hypothalamic nuclei. The brain clocks are not self-sustained oscillators – they need a daily input from either the eyes or the pineal, depending on the species. It is not known if the retinal/pineal clocks are self-sustained oscillators in the long term. Their presence is necessary for circadian rhythmicity, but a feedback signal from the hypothalamus to these structures might be necessary, too. Data so far cannot distinguish between the hypothesis that cellular clocks in the retina or pineal are autonomous clocks which entrain other parts of the system, or that a feedback loop between damped oscillators in the center and the periphery are necessary for sustained circadian output. Likewise, the ovulatory circadian rhythm may involve an interaction between cellular circadian clocks in the brain and in the ovary, or a hormonal feedback loop which does not even utilize any clock-genes and in which no single cell acts as a clock.

The idea that circadian rhythm, or similar mechanisms are involved in other aspects of biological timing is strong and some links have been made, particularly, with the timing of developmental events. Mutations of the per gene affect the developmental time in fruitflies (Kyriacou et al. 1990). The so-called heterochronic genes in C. elegans turned out to be orthologs of per and tim (Jeon et al.1999), in an organism with no circadian rhythms. However, a 90 minute cycle of chairy, which times the formation of somites in the chick embryo does not involve protein synthesis (Palmeirim and Pourquie, cited in Pennisi 1997).

To summarize, the current view of circadian rhythm generating mechanism is that it is a transcription/translation feedback loop between clock-genes and their protein products. However, the challenges to this view are coming from within the field. Some circadian rhythms are probably generated by cellular clocks consisting of two interacting loops, one being nuclear, the other cytoplasmic. As these clock-cells are organized in tissues, the communication between individual cells in that tissue confers novel properties to the circadian system of which individual cells are not capable. As most organisms, even unicells, posses more than one circadian clock, interactions between different clock-tissues allows for evolution of more complex temporal phenomena, including photoperiodic time measurement, lunar, tidal and circannual rhythms, and continuously consulted clocks. Some circadian systems are perhaps not even utilizing the individual clock-cells, but may be properties of neuroendocrine feedback loops between two or more clock or non-clock tissues (Cassone and Menaker 1984).

It is difficult to glean from the published data if this is so, but one can hypothesize that the individual variation is far greater in the properties of the whole circadian systems than in the properties of molecular circadian clocks. Period of circadian rhythmicity of the individual cells might be very similar between individuals of the same population, but the periods of the overt rhythms vary greatly, as do the emergent properties, e.g., photoperiodic sensitivity, or the critical photoperiod (e.g., Heideman and Bronson 1991, Heideman et al. 2000) due to differences in development of the whole circadian systems and hormonal influences on their properties. If this hypothesis is true, than Natural Selection will have to operate on the mechanisms of integration of the whole systems to a greater degree than on the sequences of clock-genes themselves. If cellular clocks are viewed as Lego blocks, and the circadian systems as the structures built out of these blocks, then it becomes apparent that most evolutionary changes will be in the way the blocks are put together, rather than in the shapes, sizes and colors of the blocks themselves.

Inferring Rhythmic Behavior and Physiology from Vertebrate Fossils .

I recalled what he had said of the pineal gland, and wondered what he saw with this preternatural eye. (H.P.Lovecraft, From Beyond)

From the perspective of a paleontologist, a question arises if one can infer the type of rhythmicity displayed by an animal from the fossilized remains of its bones. One asks if the fossils can tell us if particular animals were diurnal or nocturnal, and if their reproduction and migration were seasonal.

Before one starts to hypothesize about dinosaurian sleeping habits, a study of living vertebrates is in order. In an oversimplified (and Eurocentric) scheme, most of the living mammals are nocturnal, birds are diurnal, an reptiles are bimodal (dawn and dusk). But a closer look at the exceptions might be more revealing. Reptiles in the tropics are more likely to develop nocturnal habit, while at higher latitudes and/altitudes diurnality might be more common. Many diurnal birds temporarily switch to nocturnality during migration, when the production of energy favors the cool of the night. In mammals, it is mostly the small animals that are nocturnal.

Large mammals of the polar regions, like seals and walruses are diurnal, while large mammals of the Serengeti are usually bimodal.
If diurnality is taken as the default condition, the question to ask is: what adaptation to nocturnal life can be seen in the skeleton of an animal. Adaptations to nighttime activity involve adaptations to cold and adaptations to dark.

If we assume that dinosaurs were ectothermic, virtually all of them should have been nocturnal because of their large size. A large body mass dissipates heat more slowly, and is more likely to overheat. Endotherms produce their own heat but are also thought to possess more sophisticated methods of getting rid of surplus thermal energy, so if some of the dinosaurs were endotherms, they might as well have been diurnal. Also, the largest tropical mammals, like elephants, keep their core body temperature much lower than the mammalian average (20-30 C, as opposed to 37). No dinosaur was small enough to exhibit daily torpor.

Adaptations to dark involve sensory systems. There are three possible ways to adapt to life in the dark:

- evolving very sensitive eyes,
- evolving very sensitive hearing and smell, perhaps even echolocation, at the expense of largely degenerated vision, and
- evolving both very sensitive vision and other sensory modalities.

Of the three cases, the first and the third are repeatedly observed in nocturnal vertebrates. Think of owls, lemurs and cats. The second solution is employed by animals that live in caves, hollow trees or in underground tunnels. Dinosaurs were too large for this kind of fossorial habitat.

In all of these senses, increase of acuity is likely to be associated with the relative increase of size of that organ. In a fossil skeleton, enlarged ears are unlikely to be identifiable. Also, importance of the auditory acuity might be small in a world where the movements of predators and prey alike produce minor earthquakes. Detection of the enemy at a large distance might be more important, so emitting and hearing infrasound (like elephants and giraffes) could have evolved in Dinosaurs. A strong sense of smell will result in enlarged olfactory bulbs which will leave their imprints on the interior of the skull. Large eyes require large sockets. Binocular vision would also translate into a more sophisticated central processing mechanisms of visual information. Large orbits with a big overlap of visual fields, as well as large olfactory bulbs were found in the skulls of T.rex. Most bird-like dinosaurs (eg.Troodon) also had disproportionately large eyes. Were they nocturnal? Who did they hunt at night? Was their prey sleeping at the time? Where would a Brachiosaur hide for an overnight sleep? Was one guardian always awake? A careful analysis of the ecology of a certain area at a certain time might shine some light on these questions, since both temporal niches are likely to have been filled.

As for annual rhythms, they might be preserved as growth rings in the bones, reflecting the seasonal changes in food or mineral availability, UV-radiation, disease or activity (Hermann and Danielmeyer 1994). Timing of seasonal reproduction and migration is likely to have been determined by photoperiodic response. Unfortunately, living vertebrates have variable anatomical organization of the photoperiodic system. While the pineal gland and its hormone melatonin seem to be necessary in mammals, in other vertebrates pineal, parapineal organ, eyes, hypothalamus and gonads may or may not be involved. In vertebrate evolution, however, there is a trend for the pineal and parapineal organs to gradually lose a photoreceptive function and gain a secretory role.

In fish, amphibians and reptiles, pineal is a fully developed photoreceptive organ. In birds it is still responsive to light, but the histology suggests a neuroendocrine organ instead of a photoreceptor. Mammalian pineal has completely lost ability to sense light.

Parapineal organ is a highly developed “third eye” with a lens in most fish, amphibians and some reptiles (lizards, Sphenodon). In other reptiles, as well as all birds and mammals, parapineal is gone. Even pineal itself is missing in some organisms like crocodile, dugong, armadillo, anteater, sloth and pangolin, or is very small as in elephants, rhinos, manatees, whales, monotremes, marsupials and bats. The existence and size of the pineal gland and/or parapineal organ seems to correlate well with the climate and latitude.

Global species, like horses, cows, sheep and rabbits have large pineals. Polar animals, like seals, sea lions and walruses tend to have the largest pineals. This fact, together with the hypothesis that the pineal is somehow involved in thermoregulation, prompted Roth and Roth (1980) to argue that dinosaurs were cold-blooded and restricted to tropical climates, since most Dinosaur skulls do not show evidence of the presence of the pineal-parapineal complex. In all vertebrates except primates, pineal gland leaves an imprint on the inside of the skull on the roof of the brain. Parapineal lies in a hole in the skull called the pineal foramen. Only in Diplodocids there was evidence for the existence of the parapineal organ, and only in some bird-like Dinosaurs for the pineal itself. In any case, existence of parapineal foramina is easily perceived in fossil skulls, and it is the study of living organisms’ roles of these organs that needs to be correlated with the daily and seasonal rhythms, as well with thermoregulation.

The circadian clock, of which pineal is a part, is also involved in orientation by sun compass, night-sky orientation and magnetoreception. These mechanisms, although useful for all animals, are particularly necessary for long distance migrants, as some Dinosaurs were shown to be. A wide variety of animals has deposits of magnetic ferri-oxide thought to be involved in magnetoreception (Wiltschko and Wiltschko 1995). In vertebrates these deposits are usually concentrated within the ethmoid bone where they are innervated by the ophthalmic branch of the trigeminal nerve. I t is likely that Dinosaurs possessed these deposits, and it would be very interesting to compare the species with respect to quantity, location, particle-size and orientation of biomagnetite. Unfortunately, study of this phenomenon in living animals is still in its pioneering stages, so any theorizing concerning Dinosaurs would still be pure speculation.

In summary, analysis of vertebrate fossil skulls in light of relative sizes of sensory organs including eyes, olfactory bulbs, pineal and parapineal organs and magnetite particles, can give us insights into spatio-temporal physiology, ecology and behavior of Dinosaurs and other extinct vertebrates.

Tests of Adaptive Function.

As there are two main hypotheses regarding adaptive function of biological rhythms, there are also two lines of research involved in testing these hypotheses. The hypothesis that the primary role of a circadian clock is to orchestrate physiological and biochemical functions and events within a body has usually been tested by looking at longevity of either normal or clock-altered organisms placed in unnatural light cycles. For instance, fruitflies kept in different periods of light-dark cycles, as well as various clock-mutants have been reported to have different lengths of lifespans (Pittendrigh and Minis 1972). Similar findings were obtained form a study of hamsters (Hurd and Ralph 1998). The fact that breeding 600 generations in constant darkness did not lead to the loss of any circadian function in fruitflies adds another argument in support of this hypothesis (Sheeba et al. 1999).

The hypothesis that behavioral adaptations to timing of environmental events, including the temporal organization of natural enemies, has also been recently addressed. In cyanobacteria, colonies of various period mutants were subjected to competition assays in various lengths of light-dark cycles (Ouyang et al. 1998). Invariably, the strain whose endogenous period more closely matched that of the environmental cycle won the competition.

In rodents, lesions of the suprachiasmatic nucleus renders these animal arrhythmic even in light-dark cycles. In field conditions, lesioned individuals were more susceptible to predation than their intact conspecifics in the same area. This effect was greater when the predator pressure was greater (DeCoursey et al. 1997, 2000). These data suggest that correct timing of activity is crucial for survival of prey species. However, these studies do not address the question if, in absence of the clock, organisms could have evolved alternative mechanisms of temporal control.

In my opinion, the best way to study adaptive function of circadian clocks is to study coevolution of temporal parameters in two or more species of natural enemies. For instance, one can study circadian rhythmicity in a venomous snake, e.g., rattlesnake and its venom-resistant prey, the ground squirrel. In areas of sympatry, at what times of day are the two species active, and does that differ from the populations in allopatry? Is there a circadian rhythm in snake’s venom production, venom composition and toxicity, amount of venom injected in a bite, inclination to bite in response to a stimulus? Likewise, is there a circadian rhythm of resistance to venom and in evasive behaviors in the squirrels? Are those rhythms different in allopatry? Who is “winning”: the predator or the prey?

The same kind of questions can be asked in other systems, e.g., resistant predator and poisonous prey (garter snake and tiger salamander); resistant predator and venomous prey (desert mouse and scorpion); venomous defender and non-resistant intruder (guard honeybee and Death’s Head Sphinx Moth); non-resistant host and venomous parasitoid (American cockroach and it’s wasp prey), etc. Collectively, results of these experiments would give insight into the dynamics of evolution of circadian clock properties in their adaptive contexts.

A more complex system, one involving more than two species, might be more difficult to study, but would be even more informative. For instance, there is a case (Sara Oppenheim, personal communication) where a single specialist wasp parasitoid (Cardiochiles nigriceps) lays its eggs in larvae of two closely related moth species Heliothis virescens (HV) and Heliothis subflexa (HS). The two moths inhabit two very different plant hosts: HV feeds on tobacco, tomato and cotton, HS only on a Physallis plant. The host plants synthesize their deterrent chemicals (e.g., nicotine) evenly throughout the day. However, they show a circadian rhythm in synthesis of volatile compounds induced by the insect herbivory. These volatiles attract the wasps to the plant which carries the moth larvae. Plants emit different quantities and compositions of volatiles dependent on the species of moth which is attacking them. Wasps, in turn, are active bi-modally during the day – morning and evening only. HV lives on the surface of the leaf and is very vulnerable to the attacks of the parasitoid. On the other hand, HS quickly bores its way into the seed lantern of the plant where the wasp cannot reach it. A tobacco plant has enough leaf surface to accommodate a very large number of HV, but the Physallis plant has only a limited number of lanterns available at any time. It is not known, but it would be very interesting to discover, if the two moth species have evolved different temporal aspects of their biology. For instance, do HV larvae all emerge simultaneously in large numbers and find safety in numbers, while HS emerge one at a time as each individual needs time to search for and find a lantern? At what time of day do the larvae emerge, climb, feed, drop on the ground and pupate? Is there a difference in the sensitivity to light in two species as the HS hidden in a lantern is more protected from environmental light than the HV which sits out in the open? If there are differences in clock properties do they also translate into differences in developmental timing, frequency of courtship song, photoperiodic time-measurement and the ability of one of the species to invade higher latitudes? How are the plants, the wasp, and the two moths tracking each other in time – who is “winning” the race around the circadian clock? Can the changes in circadian properties be considered a part of the mechanism by which the two moth species speciated from each other in relatively recent past? Answers to these and similar questions would provide great insights into evolution and adaptive function of circadian systems.

Effects of clocks on evolution.

We have so far seen that there is individual variation in timing mechanisms (Aschoff 1998); that this variation is heritable; that timing is an important adaptive function, hence that clocks are products of evolution by natural selection. Let us now see if the possession of a clock can, in turn, direct or restrict the possible paths of further evolutionary change.

As noted above, it seems that biological clock mechanisms, perhaps even the same as circadian ones, are involved in timing of developmental events (Saunders 1972, Kyriacou et al. 1990, Moore et al. 1998). From this one can predict that changes in circadian clock properties will also have an effect on embryonic development, and vice versa. Thus adaptive changes in behavioral timing may be constrained by the needs of normal development, and heterochronic mechanisms of evolution might effect a change of fitness of the adults due to the change in physiological or behavioral synchronization.

In insects, developmental events are controlled by hormonal communication involving prothoracic glands and gonads (Nijhout 1994, 1999). Prothoracic glands are sites of circadian clocks in some insects (Vafopolou and Steel 1991, 1998). In some systems, a wasp parasitoid injects a virus into its moth victim (egg or larva) resulting in gonadectomy. The result is a change of timing of developmental events and disruption of pupation in the end. Is it possible that the lack of gonadal hormones broke one part of the feedback loop of the timer responsible for development?

As we have noted several times so far, circadian clocks are also involved in time measurement at other temporal scales from hours to years. For instance, mutations in fruitfly per gene change not just the period of circadian rhythms of behavior but also ultradian frequencies of the courtship songs (Dowse et al. 1987, Kyriacou and Hall 1980, Kyriacou et al. 1993). Likewise, sensitivity to olfactory cues is under circadian control (Krishnan et al. 1999). Although these mutations might not alter the timing of courtship activity during the day (this morning peak of sexual activity does not seem to be controlled by the PER-based mechanism), the changes in song frequency, receptivity to the song frequency, and timing of sensitivity to pheromones might greatly reduce the chance of a wild type and a mutant actually recognizing each other as mates and mating in a mixed population setting, leading to sympatric speciation via behavioral and temporal isolation due to a single nucleotide change.

On the other end of the spectrum, it is possible to construct a model in which a two-oscillator system measuring photoperiod (Warman and Lewis 1997) and another three-oscillator system controlling a free-running circannual rhythm interact to control precise timing of emergence of 17- and 13-year periodic cicadas (Williams and Simon 1995).

Likewise, many changes which various animals underwent under domestication, e.g., albinism, temperament, loss of seasonality, change in developmental time and rate of maturation, etc., point to changes in the clock systems under artificial selection (e.g., Trut 1999).

Can we go further? Circadian clocks are ubiquitous in all multicellular and many unicellular organisms. They provide a whole range of adaptive mechanisms involving development, physiology and behavior. Is it possible to have life without clocks? In my opinion, and data are needed to disprove it, without multi-oscillator circadian systems there would be no possibility for Life to invade oceanic surface, intertidal and terrestrial environments. Some components may be secondarily lost, but the process of invasion necessitated the presence of functioning circadian, lunar, tidal and photoperiodic clocks. Back in depths of the ocean, some kind of clock, not necessarily circadian, would be necessary for internal synchronization of complex organisms, and without such a timer, there would be no complex Metazoa on Earth. This leaves the bottom-dwelling microorganisms as the only organisms which do not need a clock, but will still exhibit some kinds of biochemical cycles, as life itself is defined by cycles (Bonner 1993, Kauffman 1993, 1995, Goodwin 1963, Maynard-Smith and Szathmary 1999).

If we go to another planet and find something that might be alive, how can we decide if it really is. Does it take energy from the environment, stores it, cycles it, uses it and dissipates it? Does it grow and reproduce? Does the offspring resemble parents? Is there a diversity of organisms on the planet? One more question: Is its environment periodic and does it have innate cycles corresponding in period to the environmental cycle? If yes, it is alive, as it possesses an universal adaptation which non-life cannot acquire or evolve. Endogenous rhythmicity is a diagnostic property of Life, more so than the underlying chemistry, as even living forms which do not use DNA as hereditary material, or are even not carbon-based, will still cycle in sync with the star and the moon of their native planets.

Related:

Circadian clock without DNA–History and the power of metaphor
Basics: Biological Clock
The Clock Metaphor
The New Meanings of How and Why in Biology?
Some hypotheses about a possible connection between malaria and jet-lag
Evolutionary Medicine: Does reindeer have a circadian stop-watch instead of a clock?
The Mighty Ant-Lion
Are Zombies nocturnal?
City Of Light: Insomniac Urban Animals
Me and the copperheads–or why we still don’t know if snakes secrete melatonin at night
Diversity of insect circadian clocks – the story of the Monarch butterfly
Biological Clocks in Protista
Do sponges have circadian clocks?
Daily Rhythms in Cnidaria
Carolus Linnaeus’s Floral Clocks
Clock Classics: It All Started with the Plants
Chestnut Tree Circadian Clock Stops In Winter
Flirting under Moonlight on a Hot Summer Night, or, The Secret Night-Life of Fruitflies
Too Hard for Science? Centuries to Solve the Secrets of Cicadas
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?

Today my guest is Tanya Lewis (homepage, blog, Twitter), a Graduate Student in Science Communication at the University of California, Santa Cruz.

Welcome to A Blog Around The Clock. Would you, please, tell my readers a little bit more about yourself? Where are you coming from (both geographically and philosophically)? What is your background? Any scientific education?

I guess I should start with where I spent ¾ of my life so far: Hawaii. I grew up on the Big Island, in a cowboy town (yes, these exist in paradise). I spent much of my childhood romping, or more often, running, around mountains like lofty Mauna Kea, sun-drenched beaches, and the gravel track at my high school.

But I couldn’t wait to get off the rock and explore “the Mainland” U.S. I attended Brown University, where I studied biomedical engineering. A fascination with the brain led me to work in a lab developing a brain-computer interface known as BrainGate . It’s an implantable chip that records brain signals and decodes them to enable people with paralysis to control prosthetic devices. After graduating, I knew I wanted to spend time abroad, so I applied for a research fellowship to go to Germany. I worked in a lab there studying how primates encode hand movements.

At some point, I realized I enjoyed explaining my work way more than the work itself. A little fairy spoke to me in the night and told me to become a science writer. So I did – I joined the Science Communication Program at the University of California at Santa Cruz, where I am currently. It’s been a moray ever since.

Tell us a little more about your career trajectory so far: interesting projects past and present?

In my brief but thrilling science journalism career, I’ve worked at a news office at Stanford, the local newspaper The Santa Cruz Sentinel, and now at the SETI radio show “Big Picture Science” – each an adventure of its own. This summer I’ll be venturing into the wonderful world of online science journalism, working for Wired.com in San Francisco.

In my classes at UCSC, I’ve done both news writing and long-form writing. Features are probably my favorite at this point, because of the freedom to choose a topic of interest and explore it in depth, creatively. Right now I’m working on a feature about underwater volcanoes, a subject near and dear to me, having grown up near a very active volcano (Hawaii’s Kilauea volcano). It’s fun getting to learn about volcanology, while vicariously experiencing the mysterious volcanic deep-sea landscape.

What is taking up the most of your time and passion these days? What are your goals?

In my graduate program, we just started a unit on investigative reporting and multimedia. So I’m splitting my time between hard-nosed Bob Woodward-esque reporting and peering through a camera lens. It’s a great mix, and looks to be a lot of fun. Meanwhile, I’m getting a taste of radio (to use a little synesthesia), working on the science radio show “Big Picture Science.” I’m kind of a closet filmmaking geek, and I enjoy the creative process of writing/producing/editing a project, so this will be a great adventure. Plus, the show’s hosts, Molly Bentley and Seth Shostak, are a bundle of fun to work with.

My career goal is to work in a collaborative journalism environment (such as at a science magazine or online site/blog), on stories or projects that allow me some creative freedom in the choice and handling of topics. At some point, I could see myself freelancing, for the flexibility of the lifestyle. But right now, the idea of doing it fulltime slightly terrifies me. I want enough job stability so I can realize the instability of my interests.

What aspect of science communication and/or particular use of the Web in science interests you the most?

Feature writing (online or in print) and documentary film both appeal to me, but online media is the way of the present (never mind the future). I find blogging a fun form of journalism, and one I’d like to explore more. As e-readers continue to improve, I foresee more interactivity in the act of reading. Remember those “Choose your own adventure” books? Maybe we’ll develop something akin to that, where you can easily navigate science content of your choosing, while retaining something of a narrative structure. Just a thought. I also think we’ll get better at integrating video and audio into written journalism, so it’s less distracting and more illustrative. I don’t think the written word will fall out of style anytime soon, but we will need to work hard to keep people invested in it. Hopefully I’ve kept you invested in reading this far!

How does (if it does) blogging figure in your work? How about social networks, e.g., Twitter, Google Plus and Facebook? Do you find all this online activity to be a net positive (or even a necessity) in what you do?

Right now, I’m ashamed to say my blogging presence has been somewhat lacking of late, ironically because I’ve been spending all my time studying journalism. But I contribute sporadically to our class blog, “The Crashing Edge: Current Waves of Central Coast Science”. I’ve also done some blogging at conferences, such as this year’s Science Online meeting and at last year’s American Geophysical Union Fall Meeting.

The social networks I primarily use are Twitter and Facebook. I tend to use Facebook more for personal communication, and Twitter strictly as a professional platform to share ideas in science and science journalism. I have found Twitter a useful place for keeping current with science news and immersing myself in the commentary of the science journalist community.

When and how did you first discover science blogs? What are some of your favourites? Have you discovered any cool science blogs by the participants at the Conference?

Blogs are a somewhat recent addition to my consumption of science literature. In high school and college, I tended to read scientific journal articles, popular science magazines (e.g. Scientific American, Popular Science), and The New York Times. The science blogs I read these days vary, though some of my favorites are Ed Yong’s Discover blog “Not Exactly Rocket Science” and the Scientific American Blog Network blogs (and I’m not just saying that for brownie points!). I tend to read individual blog posts (mentioned on Twitter or elsewhere) more than reading specific blogs every day, however. The Knight Science Journalism Tracker is one I try to read more regularly, though.

What was the best aspect of ScienceOnline2012 for you? Any suggestions for next year? Is there anything that happened at this Conference – a session, something someone said or did or wrote – that will change the way you think about science communication, or something that you will take with you to your job, blog-reading and blog-writing?

This being my first ScienceOnline, and having no baseline with which to compare it, I can confidently say it was a fantastic conference. Or unconference. I think the best aspect of it for me was the egalitarian and collaborative atmosphere, where you could sit in a room with a New York Times reporter or all-star blogger and feel free to converse as peers. Some of the sessions which stood out to me were Deborah Blum’s and David Dobbs’s session on shape and music in longform writing (see my Storify post), and the session on Women in Science Blogging (see here). The dinner banquet with storytelling by The Monti was good fun, too. I came away inspired by the many scintillating conversations I had with other journalists and scientists at the various social events, in the coffee room, or even on the bus. I liked the format, the only improvement I can think of is to get the word out to more journalists and scientists about this terrific event. I definitely hope to attend next year, if possible. Aloha, a hui ho!

Thank you for the interview. Hope to see you next year!

——————————————————————————-
In the (in)famous  journal called “Medical Hypotheses” Kumar and Sharma [1] propose that jet-lagged travellers may be more susceptible to getting infected with malaria. They write:

Rapid travel across several time zones leads to constellation of symptoms popularly known as “jet lag”, caused primarily due to mismatch between the timing of circadian clocks of the traveller and the external periodic environment. It is often seen that the jet-lagged individuals who visit their family and friends in areas endemic to malaria have an enhanced susceptibility to malarial infection than the local residents. It would therefore be interesting to explore whether increased susceptibility to malarial infection among the visitors has anything to do with their state of jetlagged.

Indeed an interesting hypothesis. Of course, the travelers may also be less resistant to malaria than the locals, or less likely to have a life-style and behavioral patterns conducive to avoiding the mosquito bites, something that may be “second nature” to the locals. They continue:

Individuals with moderate to severe skin response to mosquito bite are largely protected against mosquito borne malaria because itch alerts an individual to mosquito bite and prepares him/her to take necessary precautions to prevent mosquito bite. Itch in an individual follows a diurnal pattern, and it is about hundred folds higher during midnight than midday. A hundred fold increase in itch sensitivity is viewed as a crucial preventive measure against mosquito bites, as this coincides with the midnight flight activity peak of female Anopheles mosquitoes, when she sucks blood from the host after mating peaks in the evening to raise her progeny. Normally individuals residing in endemic areas have their daily peak of itch sensitivity overlapping with the peak – biting phase of female Anopheles mosquitoes. As a result, they are relatively well protected against malarial infection.

Interesting idea: if you are sensitive to bites at the time when no mosquitoes are flying and are not sensitive to bites at the time when mosquitoes are flying, you may not get to squash that mosquito in time to prevent the Plasmodia to be injected into your bloodstream. Additionally, a jet-lagged individual may experience a peak of body temperature at night. Mosquitoes, among else, home in on the warmth of their victims. Thus, jet-lagged individuals may be warmer than the surrounding locals at midnight and thus more attractive to mosquitoes at that time.

On the other hand individuals visiting endemic areas from different time zones, particularly during the first couple of days are under the state of jet lag, and their peak protective daily behavioural itch sensitivity lies out of phase with the biting peak of female mosquitoes. Therefore, such individuals are at a greater risk for sustaining malaria compared to the residents. Thus from chronobiological perspective one is of the opinion that a person can be protected against malaria by appropriately adjusting circadian clocks regulating itch sensitivity to the periodic environment. We hope that recent developments in circadian biology will help us predict extent of adjustments necessary in a new environment, which can then be of paramount importance for the protection of jet-lagged travelers to endemic regions against malaria. Some protection against malaria in the chronotherapeutic procedures such as melatonin administration, light therapy, scheduled physical exercise, maximum exposure to new environment during vector free times, social interactions, and appropriate food habits, are a few recommended preventive measures for travelers visiting a malaria endemic areas, in addition to malarial antibiotic prophylaxis.

Sounds like good advice, although the administration of melatonin is always an iffy question. However, this hypothesis got my mind all twirling and I came up with some hypotheses of my own. However, it is important to distinguish between different kinds of hypotheses regarding a putative link between jet-lag and malaria. They suggest that jet-lag may:

1) affect the rate/ease of infection with malaria,
2) affect the symptoms of malaria in an infected individual,
3) affect the ability of the body to fight off the infection,
4) affect the effectiveness of treatments, and
5) affect the likelihood that the infected individual will spread the disease to others.

The Kumar/Sharma hypothesis is clearly of the #1 type. I will look more at other types of hypotheses – those that apply to already infected individuals. For that, let’s first go quickly through the basic biology of malaria.

Plasmodium Falciparum (source unknown - let me know if you find out)

Malaria is caused by a protist in the genus Plasmodium. While Plasmodium falciparum is the most common species, three or four other species are also causes of malaria in humans, and dozens of other species cause malaria or malaria-like diseases in other animals, including mammals, birds and reptiles.

Plasmodium is transmitted through bites of several species of mosquito from the genus Anopheles. Once injected into the final host (e.g., human), the plasmodia remain in the skin for several hours, then migrate to lymph nodes, spleen and liver where they undergo several transformations. The final stage – the gametocyte – migrates into the red blood cells. Inside each red blood cell one can find a large number of plasmodia, hiding there from the immune system of the host. The whole life-cycle lasts several days, even weeks to complete.

Anopheles (source unknown)

All the plasmodia burst out of red blood cells simultaneously. Enormous number of plasmodia suddenly released into the blood overwhelms the immune system of the host, allowing the plasmodia to survive unscathed for quite a long time. This time is sufficient for them to invade blood vessels in the skin where, if they are lucky, a mosquito will bite and the plasmodia can invade the mosquito again and search for the next host.

The bursting of red blood cells triggers high fever and sweating. High temperature, high carbon-dioxide, as well as some odors [2] present in the sweat are all highly attractive to mosquitoes, rasing the probability that the host will get bitten. In some species of Plasmodium (like P.falciparum), the bursting of red blood cells occurs every night. In some species of Plasmodium, the resulting fever occurs every two nights and in some every four nights (rarely three), causing, respectively, tertian and quartan fevers. Tertian and quartan malaria are treated by chloroquine, while falciparum malaria is treated by quinine, mefloquine or halofantrine.

Plasmodium in a red cell (source unknown)

Obviously, from the perspective of a Plasmodium, timing is crucial. First, it is important to errupt in synchrony. Yet, hidden inside red blood cells, plasmodia cannot communicate with each other. Second, it is important to time the eruption in such a way as to maximize the probabilty that some of the gametocytes will be picked up by mosquitoes. Thus, it is important for the eruption to occur at the time of day when mosquitoes are most actively foraging for blood.

How do the Plasmodia solve the problem of timing? This is where circadian biology comes in [3,4,5]. Plasmodia residing inside red blood cells use the time-clues generated by the host. More specifically, they key onto the nightly release of melatonin by the pineal gland. Melatonin is practically undetectable in the blood during the day and the concentrations rise steeply in the evening remaining high for the duration of the night (exact patterns differ between vertebrate species), then dropping again at dawn.

Plasmodium falciparum life cycle (source unknown)

Plasmodia have melatonin receptors [3]. Interestingly, unlike melatonin receptors in vertebrates which are nuclear receptors, the receptors in Plasmodia are membrane receptors. Membrane receptors are much faster than nuclear receptors which is important when a biological event has to be timed with precision.

However, the plasmodia do not destroy the red blood cell immediately after receiving the melatonin signal – that would be too early in the evening for the timing to be adaptive, as the mosquitoes are still too busy looking for mates and mating at that time. Instead, the plasmodia use their own circadian clocks to measure the exact timing of eruption.

In a way, it appears that the host melatonin signal entrains (synchronizes) the clocks in plasmodia, and then the Plasmodium clock determines the phase (exact timing) for the eruption out of red blood cells.

Different species of Anopheles and even geographically distinct populations of the same species have different times of peak foraging (biting) activity. In each geographical region, the local population (or species) of Plasmodium evolved the timing of eruption to match that of the local mosquitoes.

Let’s now introduce another player. Apart from the parasite (Plasmodium), the host (a vertebrate, e.g., a human), and the vector (mosquito), one should also consider the predator – insectivorous bats that hunt for mosquitoes. The way that the malaria literature tends to think about timing can schematically be presented like this:

Timing of activity: bat vs. mosquito vs. Plasmodium vs. human

There is an assumption that plasmodium eruption, human fever, mosquito foraging and bat hunting are all synchronous. We have already looked at this from the perspective of the Plasmodium – it is adaptive for the Plasmodium for the three bottom lines to be accurate, i.e, that the parasite, the host and the vector are in synchrony. This also means that this is maladaptive to humans. It is also maladaptive to mosquitoes whose fitness does suffer somewhat if they are loaded with parasites.

On the other hand, it is maladaptive for mosquitoes and plasmodia, and adaptive for humans and bats, if the peak hunting time for bats coincides with the peak foraging time of mosquitoes. More these two events are in sync, more mosquitoes will get eaten, thus less plasmodia will get into a new host and less humans will get infected.

The dynamics of the timing relationship between the four species can be described as an Evolutionary Arms-Race Around The Circadian Clock. While some of the players will try to maximize their fitness by achieving synchrony, the other players maximize their fitness by avoiding synchrony with each other. This can be depicted, for bats and mosquitoes, like this:

Anopheles vs. bat arms-race around the clock

In this case, mosquitoes evolve to forage at later times of night, and bats evolve to track the mosquitoes by hunting later at night.

This can go on back and forth endlessly. But, and here is a big “but”. This model is quite oversimplified as it posits only four players and for each player an absolute loyalty to the other three. But is the real world that simple?

Plasmodium species are pretty host-specific. Species that thrive inside humans, may not thrive or even survive inside the bodies of other animals and vice versa. So, the parasite is pretty loyal to its host. It is also completely dependent on Anopheles – it will most likely not survive inside a different kind of mosquito.

The same mosquito that usually bites a human will happily take a blood meal from another animal. This is actually used as one of the prevention techniques: a village is surrounded by fields full of cattle, sheep, goats, horses, donkeys or camels. The mosquitoes coming out of the woods at night encounter these animals first and get satiated with blood before they ever encounter humans. The animals themselves do not get sick.

Bats are unlikely, in my opinion, to be specialized on Anopheles as their only prey. If there are no mosquitoes around, they will happily hunt other insects (and the tropical regions where malaria is common are swarming with many species of insects!). I think that involvement of bats in the arms-race is the weakest aspect of the hypothesis. Here are four basic types of bat hunting activity that are theoretically possible:

Bat activity patterns

The hypothesis suggests that bats mostly fly around midnight when the mosquitoes are most active, i.e., the bats are winners and mosquitoes loosers in the arms-race (A). If the peak is at some other point during the night, that would suggest that bats are involved in the arms-race but the mosquitoes are currently winning (B). This may also suggest that bats highly prefer some other type of prey. The bats may be active throughout the night (C) which seems most likely. Finally, the bats may have a bimodal distribution: a lot of hunting early and late at night with a siesta right around midnight (D).

This would suggest that mosquitoes have found their best temporal niche in that dangerous world, i.e, although the bats are not involved in the arms-race, the mosquitoes are and are thus winners, without making the bats “loosers” in the process.

What is the real story? I don’t know. Obviously, it is possible to monitor patterns of bat activity [6,7], yet it still needs to be done in regions in which malaria is common. Some of the bats studied in the USA follow predominantly pattern C from the figure above, and it is not too far-fetched to hypothesize that all bats everywhere have similar patterns:

Bat activity

What are the Anopheles patterns? While they search for blood around midnight, that is not the only time they are flying around.

Most of the early part of night is spent looking for mates, mating and laying eggs [8]. Thus, they are easy pickings for bats at times when they are not actively seeking humans. It appears that becoming diurnal is not a good option for Anopheles in the tropics – perhaps there are more birds there than bats, or the birds are more dangerous? It is not impossible for a mosquito to become diurnal – the mosquito we are used to seeing around here – the Culex – is crepuscular (dawn and dusk) and the Asian tiger mosquito is fully diurnal.

Anopheles oviposition

How does jet-lag figure in here? Apart from the hypothesis stated by Kumar and Sharma that itch sensitivity to mosquito bites gets displaced (and what I added – that temperature rhythm is also displaced), jet-lag will have other effects, too. Let’s look at possible effects it may have on people who already have malaria (and you’ll see why I had to use so much space describing all of the details of the arms-race above!).

Will jet-lag affect the way our body copes with the infection? In a jet-lagged human, there is no clear and sharp rhythm of melatonin release. Some amounts of melatonin are synthetized and secreted at all times of day. This means that the Plasmodium has lost its temporal anchor – there is no signal to use for determination of timing for eruption out of red blood cells. Thus, the gametocytes will errupt at random times – one cell now, another in an hour, another tomorrow. There is no safety in numbers any more – the human immune system is now perfectly capable of dealing with all the plasmodia in the circulation. Of course, the immune system itself may be somewhat compromised in a jet-lagged person.

Will jet-lag affect the way malaria presents its symptoms? The asynchronous eruption of plasmodia also means that there will be no abrupt onset of high fever at midnight. Instead, one may expect a continous low-grade fever. Nightly episodes of high fever are an important symptom of malaria. Will a physician with a patient who exhibits continuous low-grade fever ever suspect malaria?

Especially a physician in a country in which there is no malaria and the patient has returned home from the tropical travels and is jet-lagged from a return trip.

Will jet-lag affect the effectiveness of drug treatments? I don’t know the details of the way anti-malarial drugs work, so make sure you tell me if I get this all wrong. If the number of plasmodia in the circulation at any time is relatively small, and if the enzymatic destruction of the drug by liver is operating at a constant low rate (instead of with a circadian rhythm of its own), then being jet-lagged should enhance the effectiveness of the drugs, or even allow for the dose to be lowered.

Will jet-lag affect the ability of the patient to be a source of transmittion of the disease to others? With plasmodia erupting at all times of day and with most plasmodia being destroyed by the immune system throughout the day, it is much less likely that any will be present in the skin capillaries at just the right time – at midnight. Also, without a high fever coupled with sweating, the patient is less attractive to the mosquitoes than a malarial patient in the neighboring house who is local and not jet-lagged. Thus, the likelihood of plasmodia being picked up by mosquitoes is even smaller.

To summarize: according to the Kumar/Sharma hypothesis, being jet-lagged increases the chances for contracting malaria. On the other hand, if you already have the disease, it may be good for you to get jet-lagged! As long as you tell your physician that malaria is a serious option so the symptoms are not misinterpreted, you should be better off jet-lagged, allowing your body to fight the disease one plasmodium at a time.

Finally, as a matter of public health policy, how does one get the whole population of malarial patients in one country jet-lagged so as to reduce the transmission rates? Should hospitals induce jet-lag in malaria patients by shifting light-cycles or administering melatonin? How do the pros and cons of such treatment balance? Ah, so many hypotheses, so little data! I hope someone studies this in the future.

One last thing – notice that much of the work described above was performed by researchers outside of USA – not that it is important, but it shows that millions of NIH dollars are not neccessary for great science. Apart from a little bit of cellular physiology, most of the information comes from ecological field-work, and ALL of it is inspired by and informed by evolutionary theory. Not a single gel was run.

Now, I am not dissing molecular biology. Malaria is the only complex parasitic disease in which all players (plasmodium, mosquito and human) have their complete genomes sequenced, and much will be gleaned from such data in terms of designing better anti-malarial drugs, etc. But, as the above research shows, Big (molecular) Biology is not neccessary for findings that have a potential to seriously affect the infection and transmission rates of the disease.

References:

[1] Jet lag and enhanced susceptibility to malaria, C. Jairaj Kumar and Vijay Kumar Sharma, Medical Hypotheses (2006) 66, 671-685

[2] Fooling Anopheles: Scientists Aim to Wipe Out Malaria by Outsmarting a Mosquito’s Sense of Smell

[3] Calcium-dependent modulation by melatonin of the circadian rhythm in malarial parasites, Carlos T. Hotta, Marcos L. Gazarini,Flávio H. Beraldo, Fernando P. Varotti, Cristiane Lopes, Regina P. Markus, Tullio Pozzan and Célia R. S. Garcia, NATURE CELL BIOLOGY , VOL 2, JULY 2000, p.468

[4] Melatonin and N-acetyl-serotonin cross the red blood cell membrane and evoke calcium mobilization in malarial parasites, C.T. Hotta, R.P. Markus and C.R.S. Garcia, Braz J Med Biol Res 36(11) 2003

[5] Tertian and Quartan Fevers: Temporal Regulation in Malarial Infection, Célia R. S. Garcia, Regina P. Markus, and Luciana Madeira, JOURNAL OF BIOLOGICAL RHYTHMS, Vol. 16 No. 5, October 2001 436-443

[6] Sampling bats for six or twelve hours in each night? Esberard CEL, Bergallo HG, REVISTA BRASILEIRA DE ZOOLOGIA 22 (4): 1095-1098 DEC 2005

[7] Nightly, seasonal, and yearly patterns of bat activity at night roosts in the Central Appalachians, Agosta SJ, Morton D, Marsh BD, Kuhn KM, JOURNAL OF MAMMALOGY 86 (6): 1210-1219 DEC 2005

[8] Daily oviposition patterns of the African malaria mosquito Anopheles gambiae Giles (Diptera: Culicidae) on different types of aqueous substrates, Leunita A Sumba, Kenneth Okoth, Arop L Deng, John Githure, Bart GJ Knols, John C Beier and Ahmed Hassanali, Journal of Circadian Rhythms 2004, 2:6

#DCscitweetup in Washinton DC on April 12th.

ScienceOnlineSeattle, in Seattle on April 16th

The Story Collider, NYC, Wednesday April 18th

ScienceOnlineVancouver, in Vancouver on April 19th

ScienceOnlineBayArea, in San Francisco on April 19th

North Carolina Science Festival, April 13-29.

The Philadelphia Science Festival, April 20-29.

Grand Opening of the Nature Research Center, the new wing of the NC Museum of Natural Sciences, Raleigh NC, Apr. 20-21st.

#NYCSciTweetup, NYC, April 22nd (exact location TBA).

Science Online NYC, May 2nd.

#BoraZUofA: A thought-provoking week with Bora Zivkovic by Marie-Claire Shanahan:

Just a few weeks ago I waved goodbye to Scientific American blogs editor Bora Zikovic and thanked him for a wonderful week of talks at the University of Alberta. Somehow in just a week we’d managed to chat about science teaching, science blogs, the history of academic publishing, open-access, post-publication peer review, science on Twitter and so much more. It was exciting and exhausting, and my ideas notebook is completely full.

As part of the University’s Distinguished Visitor program, a small group of faculty from cell biology (Joel Dacks), anthropology (Bora’s brother, Marko Zivkovic) and science education (me) brought Bora to town to speak with students and faculty. No matter what the topic, the theme seemed to be: keep an open mind. Be willing to consider new ways of doing things but also remember that they might not be as they first appear….

My Week with @BoraZ by Torah Kachur:

…..The fact is that the web has changed how science is done – and Bora is evidence of that. From bloggers being way more than just men in pyjamas in their parents basement to full lab books being completed open and online for the whole world to watch. The 21st century will be driven by bloggers being the peer reviewers, open access dominating publishing houses and science being done for all the public to follow and learn.

We, the bloggers, are the nerds behind the paradigm shift in the pursuit of science. Bora will continue to advocate for more Open Access journals so that the public can engage in science and it will become more accessible to everyone. And we, at Science in Seconds will continue to be geeky and super sarcastic.

This entire time I spent with Bora laughing at jokes only a scientist could love and discussing every topic under the sun, his brother Marco – a cultural anthropologist who is studying scientist culture – was sitting there….studying us….making us his guinea pigs….and occassionally throwing out a comment about just how different the dorks of the world really are…

#BoraZUofA Linkfest: A collection of the sites and posts referenced in Bora’s talks by Marie-Claire Shanahan:

Scientific American blog editor Bora Zivkovic‘s visit to the University of Alberta was a wonderful whirlwind of talks on science education, science communication, open science, peer review and the scientific publishing industry. I’ve summarized his talks in an overview of the week. If you’re interested in a more in-depth look, Bora has also shared a list of links to the sites, posts and people he mentioned or used in his talks (or intended to use in some cases). It’s a terrific guide to exploring these issues online…

Visiting editor talks technology in education by Rachel Singer:

The internet is changing science education and communication in a remarkable way, according to a Scientific American magazine editor visiting the U of A this week.

As part of the U of A’s Distinguished Visitor Program, Bora Zivkovic will be delivering various talks on implementing technology in science education, including how to communicate research through social media, and navigating the benefits and pitfalls of scientific interaction online.

Zivkovic says the focus of his trip is to get people to reconsider science education and to promote science online….

SOCIAL MEDIA IN EDUCATION by Katelyn Hoffart and Kaitlyn Grant:

The “blogfather” of Scientific American magazine’s blog network, Bora Zivkovic, discussed the use of social media in education and research at a University of Alberta talk last week.

Zivkovic ended a week-long speaking series with a drop-in discussion on communicating research through social media. Students and staff discussed with Zivkovic the ins and outs of using blogs as personal and professional tools for research.

Blogs have brought together people from different professions and interests, including Marie-Claire Shanahan, an associate professor in the Faculty of Education who shared her experience of blog-initiated partnership to the discussion….

Skeptically Speaking #156: Beyond 42:

This week, we’re experiencing the power of stories to communicate science. Join us for Beyond 42: How Science Can Use Stories to Explain Life, the Universe and Everything. This event, recorded live in Edmonton, features Scientific American Blog Editor Bora Zivkovic, and a fantastic cast of scientists telling moving stories that communicate the wonder of science and discovery….

Teaching and learning through online science: First Bora Zivkovic (@BoraZ) talk at University of Alberta in Edmonton, Alberta, Canada (Storify) by Tim Skellet.

Changing the nature of science literacy online: Second Zivkovic (@BoraZ) talk at University of Alberta in Edmonton, Alberta, Canada (Storify) by Tim Skellet.

Navigating the benefits and pitfalls of scientific interaction online: Third Bora Zivkovic (@BoraZ) talk at University of Alberta in Edmonton, Canada (Storify) by Tim Skellet.

And, only tangentially related to the events of the week – the #arseniclife saga and the nature of the current science media ecosystem – this new paper in which I was quoted (and I am happy with the quote – if you do not have access and are interested in the context of the quote I have a PDF I can send you, just ask): To hype, or not to(o) hype by Andrea Rinaldi:

…Of course, the media landscape is extremely varied, as science blogger and writer Bora Zivkovic pointed out. “There is no unified thing called ‘Media’. There are wonderful specialized science writers out there, and there are beat reporters who occasionally get assigned a science story as one of several they have to file every day,” he explained. “There are careful reporters, and there are those who tend to hype. There are media outlets that value accuracy above everything else; others that put beauty of language above all else; and there are outlets that value speed, sexy headlines and ad revenue above all.”…

Today my guest is Rebecca Guenard (blog, Twitter).

Welcome to A Blog Around The Clock. Would you, please, tell my readers a little bit more about yourself? Where are you coming from (both geographically and philosophically)? What is your background? Any scientific education?

Hi, I’m Rebecca Guenard. I currently live outside of Philadelphia, PA with my husband and our two boys.

I have loved math and science for as long as I can remember. I have a B.S. and a Ph.D. in Chemistry.

I spent a year working for the chemical industry where I learned I was better suited for academia.

Tell us a little more about your career trajectory so far: interesting projects past and present?

I began my career in academia as an adjunct while we started our family. Then I took a permanent teaching position at Temple University. I worked at Temple for five years, teaching the large freshman lectures, as well as upper division courses for majors. At the same time I conducted research, sort of a nontraditional postdoc. My aim was to seek a tenure track position, but the needs of my family were such that I left Temple to work independently from home. Now I am part-time cruise director and part-time science writer.

The transition from academia was tough, I had been in hallowed halls since I was 17 years old. I had grown attached to the structure of the academic system. So I took a few years to concentrate on kids and figure out life outside that hierarchy. I kept my hand in chemistry while I privately tutored, but I opened myself up to new experiences. I volunteered for an organization that needed help improving communications. The experience taught me a lot and gave me the confidence to combine chemistry and communications, as I had originally intended when I left Temple.

Science writing is another form of teaching. A 50 minute lecture for a freshman class is a kind of performance; there is an entertainment factor associated with it. This is especially true for chemistry because students tend to be intimidated by the subject. A good chemistry professor pulls students in, settles their fears and while their attention is gripped shoves in as much curriculum as they can.

I have the same philosophy when I communicate science with the written word.

What is taking up the most of your time and passion these days? What are your goals?

Currently, most of my time is taken up with telling stories. I developed a blog called atomic-o-licious last summer which I am using to feel my way through science communications.

I am interested in accessibility. If you want to read science content you have hundreds of options. If you seek it out you will find it. But there are so many people who never seek out science. Maybe they are busy or intimidated, for whatever the reason science isn’t a priority. There is an extensive audience that needs to be offered different bait. It is that audience I seek with atomic-o-licious.

I would love for my blog to be like a Dave Barry column which attracts readers because it is entertaining, it makes them laugh. But there is a bonus, science is folded in among the humor.

Every day I can pull a story from my life and relate it to chemistry; I see the world through chemistry-colored glasses. And most days life just cracks me up. What a dream to have an outlet for combining the two!

Chemistry is a tough subject; readers are naturally drawn to life sciences, chemistry tends to drive people away. But I am going to draw them, gosh darnnit.

One of my goals is to expand my readership. It is creeping up slowly. I am grateful for the receptiveness of the science writing community, and I look forward to reaching a broader audience.

I am also continually pitching stories to mainstream publications to get my name in print and out to a non-science audience which might be enticed back to my blog (plus I wouldn’t mind getting paid).

What aspect of science communication and/or particular use of the Web in science interests you the most?

The Web is full of amazing science resources. Since I am most interested in creating a narrative, in telling a good story, I am focused on blogs right now. I also like blogs for aggregating information. Social media makes it so easy to share new, interesting research that is written about on blogs.

I also like the idea of having a YouTube channel, a place to create chem videos, but I need time to formulate the goals of such a channel.

How does (if it does) blogging figure in your work? How about social networks, e.g., Twitter, Google Plus and Facebook? Do you find all this online activity to be a net positive (or even a necessity) in what you do?

Aside from being a form of science communication, I view my blog as a portfolio. If you take the whole body of work hopefully you can see that I am growing and learning in the craft of science writing.

I would have zero readership without social networks. They are vital to expanding science communication. I like that social networks connect me to other science communicators.

I had a narrow view of science prior to social networks. There was the research I was doing and the research papers that I read that were close to what I was doing; who had time for anything else. With social networks I am connected to people with different backgrounds and interests and through our network they bring what they are studying to me. It is a process that still amazes me. I am exposed to so much more than I ever was before social networks.

When and how did you first discover science blogs? What are some of your favourites? Have you discovered any cool science blogs by the participants at the Conference?

The Loom is probably the first science blog I discovered, but I can’t remember how I came across it. Prior to that I mostly read science in print and on news sites. But until recently, when I came out from under my chem prof bell jar, I was oblivious to how much was available.

I ricochet throughout the web daily. I mostly visit blogs within science blog networks or stories that are brought to my attention on Twitter.

What was the best aspect of ScienceOnline2012 for you? Any suggestions for next year? Is there anything that happened at this Conference – a session, something someone said or did or wrote – that will change the way you think about science communication, or something that you will take with you to your job, blog-reading and blog-writing?

Every aspect of the conference changed the way I think about science communication. I was trained to hold on tight to information. Some of the research projects I was on were industry collaborations so the research results were proprietary, but also science is a competitive environment in which to be raised. Knowledge is power, you don’t relinquish it, that is the message that gets whispered in your ear.

There is a lesson to be learned from the difficulty the scientific community has had relaying the importance of climate change. We can’t just keep the general public out of scientific research and expect that they will suddenly snap into compliance when we discover something troublesome. Climate scientists have had to spend precious years explaining how they know what they know about climate change instead of taking steps to stop it.

This issue coupled with social media has developed a new breed of scientists who understand the need for the open communication of research. I am having to play catch-up and unlearn my training. This conference was an invaluable aid in taking those steps. All of the openness was weird at first, the twitter followers, the conference wikispace, the open access conference schedule. I felt exposed. But I met people I wouldn’t even have made eye contact with at another conference.

I had many interactions with people at scio12 that have influenced my work. I spoke with journalism veterans who gave me concrete advice on finding narratives, maintaining blogs and refining stories. I also talked to people who have been blogging longer than me and graciously extended their advice, encouragement, and support. It was a wonderful experience. I look forward to scio13!

Thank you for the interview. Hope to see you next year!

As we mentioned just the other day (May 2007), studying animal behavior is tough as “animals do whatever they darned please“. Thus, making sure that everything is controlled for in an experimental setup is of paramount importance. Furthermore, for the studies to be replicable in other labs, it is always a good idea for experimental setups to be standardized. Even that is often not enough. I do not have access to Science but you may all recall a paper from several years ago in which two labs tried to simultaneously perform exactly the same experiment in mice, using all the standard equipment, exactly the same protocols, the same strain bought from the same supplier on the same date, the same mouse-feed, perhaps even the same colors of technicians’ uniforms and yet, they got some very different data!

The circadian behavior is, fortunately, not chaotic, but quite predictable, robust and easily replicable between labs in a number of standard model organisms. Part of the success of the Drosophila research program in chronobiology comes from the fact that for decades all the labs used exactly the same experimental apparatus, this one, produced by Trikinetics (Waltham, Massachusetts) and Carolina Biologicals (Burlington, North Carolina):

This is a series of glass tubes, each containing a single insect. An infrared beam crosses the middle of each tube and each time the fly breaks the beam, by walking or flying up and down the tube, the computer registers one “pen deflection”. All of those are subsequently put together into a form of an actograph, which is the standard format for the visual presentation of chronobiological data, which can be further statistically analyzed.

The early fruitfly work was done mainly in Drosophila pseudoobscura. Most of the subsequent work on fruitfly genetics used D.melanogaster instead. Recently, some researchers started using the same setup to do comparative studies of other Drosophila species. Many fruitfly clock labs have hundreds, even thousands, of such setups, each contained inside a “black box” which is essentially an environmental chamber in which the temperature and pressure are kept constant, noise is kept low and constant (“white noise”), and the lights are carefully controlled – exact timing of lights-on and lights-off as well as the light intensity and spectrum.

In such a setup, with a square-wave profile of light (abrupt on and off switches), every decent D.melanogaster in the world shows this kind of activity profile:

The activity is bimodal: there is a morning peak (thought to be associated with foraging in the wild) and an evening peak (thought to be associated with courtship and mating in the wild).

The importance of standardization is difficult to overemphasize – without it we would not be able to detect many of the subtler mutants, and all the data would be considered less trustworthy. Yet, there is something about standardization that is a negative – it is highly artificial. By controlling absolutely everything and making the setup as simple as possible, it becomes very un-representative of the natural environment of the animal. Thus, the measured behavior is also likely to be quite un-natural.

Unlike in the lab, the fruitflies out in nature do not live alone – they congregate with other members of the species. Unlike in a ‘black box’, the temperature fluctuates during the day and night in the real world. Also unlike the lab, the intensity and spectrum of light change gradually during the duration of the day while the nights are not pitch-black: there are stars and the Moon providing some low-level illumination as well. Thus, after decades of standardized work, it is ripe time to start investigating how the recorded behaviors match up with the reality of natural behavior in fruitflies.

Three recent papers address these questions by modifying the experimental conditions in one way or another, introducing additional environmental cues that are usually missing in the standard apparatus.

Flirting

In the first paper, Nocturnal Male Sex Drive in Drosophila (Current Biology, Volume 17, Issue 3 , 6 February 2007, Pages 244-251), by Fujii, Krishnan, Hardin and Amrein, the problem of isolation was dealt with. In order to do this, a different apparatus had to be used, in this case a bunch of petri-dishes placed under the watchful eye of a video camera:

Two flies at a time were placed in each petri-dish: either two males, two females or one male and one female. Their general locomotor activity was compared to that of isolated insects of both sexes. In addition, some more concrete behaviors – “close-proximity” (i.e., two individuals approaching each other), courtship and mating were monitored as well.

So, what did they find? Putting two males or two females together did not change the activity patterns much. But putting one male and one female together provoked a large change of behavior – most of the approaches, courting and mating occured during the night!

Here are individual males:

And here are male-female pairs:

Additionally, they found that the flies revert back to their standard patterns if placed back into isolation (so being virgin vs. experienced does not matter and the shift in patterns of behavior is not permanent).

Also, by entraining males and females 11 hours out of phase with each other and then placing them together, they discovered that the males drove the couples’ behavioral patterns – the pair always assumed the phase of the male.

Finally, experiments with various genetic knock-outs and mutants (I’ll spare you the tedious details) revealed that a) the males drive the pattern due to their perception of the females’ smell and b) intact circadian pacemakers in both the brain and the antennae (the fly equivalent of the olfactory bulb in some sense) are necessary for the shift of behavior to a nocturnal pattern.

Moonlight

So, if the first paper suggests that the smell of virgin females can lure males to get active in pitch darkness, would a low-level light at night also encourage flies to stay up all night and party? The role of dim light during the nights was studied in the second paper, Moonlight shifts the endogenous clock of Drosophila melanogaster (PNAS, February 27, 2007, vol. 104, no. 9, pp. 3538-3543) by Wolfgang Bachleitner, Lena Kempinger, Corinna Wülbeck, Dirk Rieger, and Charlotte Helfrich-Förster.

In an earlier paper from the same lab, shutting down the activity in one of the clock genes eliminated the morning peak of activity, but the evening peak remained for quite a few days (even weeks) afterwards (does that mean that eating is less important than mating?), suggesting that the two peaks are driven by different clocks.

In this paper, the authors used an artificial light equivalent in intensity to a quarter-moon light. They compared activity patterns as well as patterns of clock-gene expression in standard light-dark cycles, in constant dark, in constant moonlight, and in a light-moonlight cycle.

Both the activity and the gene expression changed dramatically when moonlight was present. The morning peak started earlier, during the latter portion of the moonlit night, while the evening peak extended into the early portion of the next moonlit night:

The pattern of cycling of clock-proteins followed the same pattern as activity – advanced (and broadened) in the part of the brain thought to house the morning oscillator and delayed (and broadened) in parts of the brain thought to house the evening oscillator (though the literature is still not clear on their exact location).

Furthermore, deletion of an important photopigment (cryptochrome, which is not a clock gene in flies) only slightly raised the treshold of sensitivity to light – the activity patterns changed in the same way as in wildtype flies once the intensity of moonlight was raised to 0.5 lux. Being a blue-light pigment, cryptochrome may be imporant in detection of changing spectra during dawn and dusk and thus involved in the measurement of photoperiod (daylength).

But, deletion of a gene that results in lack of compound eyes (but not ocelli) made the flies blind to moonlight (not daylight, though). So, light detection by compound eyes is necessary for the changes in activity patterns in the presence of moonlight. Also, the peripheral clock in the compound eyes did not switch patterns of gene expression under moonlight in wildtype flies.

Hot Summer Nights

I initially intended to include another paper in this review – Integration of Light and Temperature in the Regulation of Circadian Gene Expression in Drosophila (PLoS Genet 3(4): e54 doi:10.1371/journal.pgen.0030054) by Boothroyd CE, Wijnen H, Naef F, Saez L, Young MW – but now that I have read it, I realize that it may be better to write about it on its own (and not just because it is huge, but also because it is conceptually complex) or together with another paper that recently saw some press and deserves some coverage by me as well. So, for now, yes, one can use temperature cycles to alter the patterns of fruitfly activities (and move it somewhat into the night) but that is not the main finding of the paper.

In summary, what a simple light-dark cycle in the laboratory does to isolated fruitflies is “box” their activity entirely within the light phase of the cycle. In other words, it exerts a strong masking effect of light on activity. Out in nature, presence of dim light, temperature cycles and conspecifics allows these insects to spread their activity into the night. While we still agree that the pattern, being bimodal, is that of a crepuscular animal, these new findings suggest that the fruitflies are not predominantly diurnal as thought to date, but flexible in their behavior and under some conditions even strongly nocturnal animals.

But no matter what period it was, people have read (or tried to read, or pretended they could read and understand) the magazine in its entirety, regardless of the subject matter. This includes some readers who themselves were prominent leaders in their scientific disciplines. And sometimes they’d say something about that reading habit in public. Here are two examples from anthropology.

Claude Lévi-Strauss, one of the founders of Anthropology, said, among else, this in his 1977 Massey Lecture:

Let me start with a personal confession. There is a magazine which I read faithfully each month from the first line to the last, even though I don’t understand all of it; it is the Scientific American. I am extremely eager to be as informed as possible of everything that takes place in modern science and its new developments.

To see the context in which he uttered these words, you can listen to the lecture here, read it online here, or buy it in book form here.

Alfred Gell, another prominent anthropologist, wrote this in his 1999 book (really a collection of essays) The Art of Anthropology: Essays and Diagrams, on page 24:

You can read the book online here or buy the book here.

Thanks to my brother for bringing my attention to these two quotes.

If you find similar quotes by other notable people from the past, let me know so I can post them here.

Big news of the month – ScienceOnlineNOW news and ScienceOnline2013 date:

ScienceOnline NOW!

And check out the video of ScienceOnline2012:

ScienceOnline2012 in Review [Video]

Several new ScienceOnline interviews last month:

ScienceOnline2012 – interview with Matthew Hirschey
ScienceOnline2012 – interview with Matt Shipman
ScienceOnline2012 – interview with Jessica Morrison
ScienceOnline2012 – interview with Elizabeth Preston
ScienceOnline2012 – interview with David Shiffman
ScienceOnline2012 – interview with Roger Austin
ScienceOnline2012 – interview with Katie Cottingham
ScienceOnline2012 – interview with Josh Witten
ScienceOnline2012 – interview with Michele Arduengo
ScienceOnline2012 – interview with Jamie DePolo
ScienceOnline2012 – interview with Chuck Bangley

I republished a few posts from the old archives:

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?
Biological Clocks in Protista
Do sponges have circadian clocks?
Daily Rhythms in Cnidaria

Previously in the “Best of…” series:

2012

February
January

2011

December
November
October
September
August
July
June
May
April
March
February
January

2010

December
November
October
September
August
July
June
May
April
March
February
January

2009

December
November
October
September
August
July
June
May
April
March
February
January

ScienceOnline2012 in Review from steadyfilm on Vimeo.

Today my guest is Chuck Bangley (blog, Twitter).

Welcome to A Blog Around The Clock. Would you, please, tell my readers a little bit more about yourself? Where are you coming from (both geographically and philosophically)? What is your background? Any scientific education?

Like a lot of us in the Carolinas, I’m a transplanted Northerner.  I grew up in the great state of Rhode Island, spent some time in Vermont, and then went back to RI where I got my B.S. in marine biology at URI.  I worked in an environmental testing lab for a bit after graduation, then had an internship with the Rhode Island state Marine Fisheries Division before budget cuts sent me south for grad school.  I joined up with the Rulifson lab at East Carolina University, where I finished off my M.S. in Biology and am now working on a PhD in Coastal Resource Management.  Basically I never grew out of my childhood shark phase and my main research interest is interactions between marine apex predators and fisheries.

Tell us a little more about your career trajectory so far: interesting projects past and present?

I’ve had the good luck to have a little experience in all three angles of fisheries research.  I got an inside view of fisheries management in Rhode Island that gave me perspective on how difficult a job that can be.  I’ve been on the academic side of it through grad school, and our lab works extensively with commercial fishermen, so I get to talk to them and get their side of the story as well.  So that’s been pretty valuable.

My Master’s work was on the feeding habits of spiny dogfish overwintering off of North Carolina, which allowed me to experiment with a non-lethal method of collecting shark gut contents and get into a little predator-prey theory.  I’ve also been involved in some other dogfish projects using acoustic telemetry, which has let me do some of the cool stuff I used to be amazed by on the Discovery Channel growing up.  Currently I’m putting together a project using a combination of fishery surveys and acoustic tracking to identify shark nurseries within the North Carolina sounds.

What is taking up the most of your time and passion these days? What are your goals?

Right now securing time, gear, and funding for that shark nursery project is keeping me busy (and up at night).  I’m still in the middle of taking classes for the PhD program as well, which takes up a lot of free time.  I’m on track to begin some pilot studies in the field this summer, so if anyone wants some (unpaid) experience working with sharks in lovely North Carolina…

What aspect of science communication and/or particular use of the Web in science interests you the most?

This is probably the really obvious answer that everyone gives, but outreach is a great benefit of your research out there online.  I’ve had people I’ve never met at conferences come up and ask me about things they saw on the blog, which is still a really surreal experience every time it happens.  It’s also put me in this community of scientists and general science fans that I would have never even been aware of otherwise.  In some ways it’s made it easier to set up new projects, because there’s this record of things I’ve done that’s out there way before any of it gets published.  But overall I’d say the people you make connections with is probably the most valuable aspect of communicating science online.

How does (if it does) blogging figure in your work? How about social networks, e.g., Twitter, Google Plus and Facebook? Do you find all this online activity to be a net positive (or even a necessity) in what you do?

Ya Like Dags? was what got me into this, and I use Twitter basically as a complement to the blog.  I do have a Facebook page, but I use that more for personal stuff so there’s really not much there.  I’ve only really scratched the surface with Google+; I have a page on there but I really only post links to new posts on the blog.  I really haven’t found the need to sit on G+ and check out posts the way I do sometimes on Twitter.  One thing Twitter has affected is the quantity (and maybe quality) of posts on the blog: where I used to have posts made up of just links on the blog, now I can just instantly make people aware of things I stumble across that are neat on Twitter.  So the overall number of posts have gone down, but the posts are all actual content now (no offense to bloggers who put out a lot of link posts).  Overall I think it’s been a net positive, and at some points I’m pretty sure the Twitter feed gets more attention than the blog.

When and how did you first discover science blogs? What are some of your favourites? Have you discovered any cool science blogs by the participants at the Conference?

Deep Sea News and Pharyngula were probably my gateway drugs into science blogs, and of course Southern Friend Science followed very quickly after them.  By seeing what other blogs those would link to, I was able to see just how big this community is and discover new blogs to read.  I started out just leaving some comments on DSN and SFS, and then I did some guest posts for my friend Matt on his Marine Music blog, which lead to me actually meeting Kevin and Andrew in real life and starting my own.  So marine blogs figure pretty heavily into the “science blogs” list of bookmarks.  Obviously I have to shout-out the other blogs on the Southern Fried network, and I think we’ve done a good job getting a lot of quality content on there.  Christie always has some really insightful posts (now at Science Sushi) and SeaMonster has a really cool mix of science and general ocean interest that I really think helps show scientists as “real people.”  Tetrapod Zoology is always a fun read because you can tell Darren has a blast writing his posts, which makes reading about a subject as potentially bland as taxonomy really enjoyable.  Some non-science ocean blogs I really enjoy include The Dented Bucket, which captures the more artistic side of commercial fishing really well, and some of the blogs about shark ecotourism (Underwater Thrills and Da Shark in particular).  I met some pretty awesome people who write outside of my discipline at Science Online, though PsySociety stands out both for having some great writing about psychology and for being able to hang with the ocean bloggers.

What was the best aspect of ScienceOnline2012 for you? Any suggestions for next year? Is there anything that happened at this Conference – a session, something someone said or did or wrote – that will change the way you think about science communication, or something that you will take with you to your job, blog-reading and blog-writing?

Honestly, ScienceOnline 2012 was probably the most well-run conference I’ve ever been to.  The venue was great, lots of opportunities for good conversation, and the only free lunch I’ve ever seen at a conference.  ScienceOnline was so smooth that it actually made me mad at other conferences I go to regularly for the way they’re run.  I think the way SciO really facilitates conversation, both through the “unconference” format and having plenty of places to sit and chat, is probably the best reason to go.  And it doesn’t shy away from the tough conversations either.  With all conferences the networking is really the best reason to go, and SciO acknowledges that and does a great job making it the main focus.  I really wouldn’t change a thing, and I’m excited for next year’s already.

Thank you for the interview. Hope to see you next year!